diff --git a/.gitattributes b/.gitattributes deleted file mode 100644 index b739161..0000000 --- a/.gitattributes +++ /dev/null @@ -1 +0,0 @@ -plutoplot/_version.py export-subst diff --git a/.github/workflows/pre-commit.yml b/.github/workflows/pre-commit.yml index 335381c..8cb0931 100644 --- a/.github/workflows/pre-commit.yml +++ b/.github/workflows/pre-commit.yml @@ -8,6 +8,6 @@ jobs: pre-commit: runs-on: ubuntu-latest steps: - - uses: actions/checkout@v2 - - uses: actions/setup-python@v2 - - uses: pre-commit/action@v2.0.0 + - uses: actions/checkout@v3 + - uses: actions/setup-python@v3 + - uses: pre-commit/action@v2.0.3 diff --git a/.github/workflows/publish-pypi.yml b/.github/workflows/publish-pypi.yml new file mode 100644 index 0000000..dd235cd --- /dev/null +++ b/.github/workflows/publish-pypi.yml @@ -0,0 +1,31 @@ +name: Build package and upload to PyPI + +on: + release: + types: [created] + +jobs: + deploy: + runs-on: ubuntu-20.04 + + steps: + - uses: actions/checkout@v3 + - uses: actions/setup-python@v3 + - name: Install build dependencies + run: | + python -m pip install --upgrade pip + pip install build twine + - name: Build package + run: | + python -m build . + - name: Upload package to PyPI + env: + TWINE_USERNAME: __token__ + TWINE_PASSWORD: ${{ secrets.PYPI_PASSWORD }} + run: twine upload dist/* + - name: Upload package to Github release + uses: alexellis/upload-assets@0.3.0 + env: + GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }} + with: + asset_paths: '["./dist/*"]' diff --git a/.github/workflows/tox.yml b/.github/workflows/tox.yml new file mode 100644 index 0000000..ed81f68 --- /dev/null +++ b/.github/workflows/tox.yml @@ -0,0 +1,31 @@ +--- +name: testing + +on: + push: + branches: + - main + - dev + pull_request: + +jobs: + tox: + runs-on: ubuntu-latest + strategy: + fail-fast: false + matrix: + python-version: [3.7, 3.8, 3.9, "3.10"] + + steps: + - uses: actions/checkout@v3 + - name: Set up Python ${{ matrix.python-version }} + uses: actions/setup-python@v3 + with: + python-version: ${{ matrix.python-version }} + - name: Install dependencies + run: | + python -m pip install --upgrade pip + pip install poetry + poetry install + - name: Test with tox + run: poetry run tox diff --git a/.gitignore b/.gitignore index 40cc3a0..0dfcd71 100644 --- a/.gitignore +++ b/.gitignore @@ -6,3 +6,4 @@ build/ dist/ .vscode/ test.ipynb +.tox diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml index ebbc739..ee31d5c 100644 --- a/.pre-commit-config.yaml +++ b/.pre-commit-config.yaml @@ -1,6 +1,6 @@ repos: - repo: https://github.com/pre-commit/pre-commit-hooks - rev: v4.0.1 + rev: v4.1.0 hooks: - id: check-added-large-files - id: check-case-conflict @@ -11,11 +11,11 @@ repos: - id: trailing-whitespace args: ["--markdown-linebreak-ext=md"] - repo: https://github.com/psf/black - rev: 21.9b0 + rev: 22.3.0 hooks: - id: black - repo: https://github.com/pycqa/isort - rev: "5.9.3" + rev: "5.10.1" hooks: - id: isort args: ["--profile", "black"] diff --git a/.readthedocs.yaml b/.readthedocs.yaml new file mode 100644 index 0000000..330c39f --- /dev/null +++ b/.readthedocs.yaml @@ -0,0 +1,11 @@ +version: 2 + +mkdocs: + configuration: docs/mkdocs.yml + +python: + version: "3.8" + install: + - method: pip + path: . + - requirements: docs/requirements.txt diff --git a/MANIFEST.in b/MANIFEST.in deleted file mode 100644 index 5b35b0d..0000000 --- a/MANIFEST.in +++ /dev/null @@ -1,2 +0,0 @@ -include versioneer.py -include plutoplot/_version.py diff --git a/README.md b/README.md index 7f1e345..d4058ef 100644 --- a/README.md +++ b/README.md @@ -1,114 +1,171 @@ -# plutoplot - Plutocode Plotting library +# plutoplot - Plutocode data loading and plotting library +![GitHub release](https://img.shields.io/github/v/release/simske/plutoplot?include_prereleases&label=Github%20Release) +![PyPI](https://img.shields.io/pypi/v/plutoplot) +[![Documentation](https://readthedocs.org/projects/plutoplot/badge/?version=latest)](https://plutoplot.readthedocs.io/en/latest/?badge=latest) +[![pre-commit](https://github.com/Simske/plutoplot/actions/workflows/pre-commit.yml/badge.svg)](https://github.com/Simske/plutoplot/actions/workflows/pre-commit.yml) +[![testing](https://github.com/Simske/plutoplot/actions/workflows/tox.yml/badge.svg)](https://github.com/Simske/plutoplot/actions/workflows/tox.yml) +![License](https://img.shields.io/github/license/simske/plutoplot) +[![Code style: black](https://img.shields.io/badge/code%20style-black-000000.svg)](https://github.com/psf/black) +[![Imports: isort](https://img.shields.io/badge/%20imports-isort-%231674b1?style=flat&labelColor=ef8336)](https://pycqa.github.io/isort/) + +`plutoplot` is a Python package for loading, analyzing and plotting data from the [astrophysical gas dynamics simulation code PLUTO](http://plutocode.ph.unito.it/). +By handling simulations as a whole and loading data only when needed (lazy loading), it is fast and easy to use. + +It features: +- Loading on data actually needed (by lazy loading in memory mapping) +- easy slicing into large datasets (e.g. plotting 2D slice of 3D dataset) +- plotting non-cartesian coordinates projected into cartesian space +- interactive plotting in Jupyter Notebooks +- CLI tool to quickly acquire information about simulations +- Access to parameters set in `definitions.h` and `pluto.ini` +- Access to simulation metadata and grid properties +- Indexing with `ijk` (like `pyPLUTO`) and `kji` (like PLUTO internally) schemes + +There is currently no support for: +- Particles +- Adaptive grids (AMR) +- 3D plotting (only plotting 2D slices of 3D data is supported.) + +To get started with `plutoplot` check out the [documentation](https://plutoplot.readthedocs.io/en/latest/) and [examples](https://github.com/Simske/plutoplot/tree/main/test). -This is a Python 3 library for plotting output data from the [PLUTO code](http://plutocode.ph.unito.it/) - -This library is under development and mostly specialized on the functionality I personally need. Nonetheless I will try to make the code as widely applicable and documented as possible. +## Installation +`plutoplot` requires Python >=3.6. Make sure for installation to install in the right environment, and/or adapt the pip commands accordingly (e.g. `pip3`). -## Requirements -``` -Python >=3.6 -numpy -matplotlib +The base version of plutoplot can be installed from Pypi with: +```bash +pip install --upgrade plutoplot ``` -## Installation -Install it with pip: +To keep the installation size small the dependencies for interactive plotting and loading of HDF5 data are declared as optional dependencies. +To install the optional dependencies use either of the following, depeding on your needs: +```bash +pip install --upgrade plutoplot[interactive] +pip install --upgrade plutoplot[hdf5] +pip install --upgrade plutoplot[interactive,hdf5] ``` -pip install git+https://gitlab.mpcdf.mpg.de/sdoetsch/plutoplot.git + +To install the current development version from this branch: +```bash +pip install --upgrade "plutoplot @ git+https://github.com/simske/plutoplot" ``` -Or download repository (as archive or with git) +## Quick Start +### CLI: check simulation info +To quickly check the status of a PLUTO simulation, you can use the `pluto-info` command line tool: +```bash +pluto-info /path/to/simulation ``` -python setup.py install +Sample: ``` +>> pluto-info test-problems/HD/Jet/01/ +PLUTO simulation at 'test-problems/HD/Jet/01' +Polar grid with dimensions (160, 1, 640) +Domain: x1: 0.00e+00 .. 1.00e+01 (Lx1 = 1.00e+01) + x2: 0.00e+00 .. 1.00e+00 (Lx2 = 1.00e+00) + x2: 0.00e+00 .. 4.00e+01 (Lx3 = 4.00e+01) +Available variables: rho vx1 vx2 vx3 prs +Data files: + Format dbl: 16 files, last time 15.0, data timestep 1.00e+00 + Format flt: 61 files, last time 15.0, data timestep 2.50e-01 -If you downloaded via git and want to keep updating via git, you can also use -``` -python setup.py develop ``` -This way the package is always read in from the git directory. +(note: depending on your Python environment, the entrypoint `pluto-info` might not be installed correctly. Check the [documentation for more details](https://plutoplot.readthedocs.io/en/latest/cli-tools)). -## Example +### Quick start in Python scripts / Jupyter notebooks ```python import plutoplot as pp +``` +#### Basics +Simulations can be loaded by just providing the path to the simulation directory (directory with `definitions.h` and `pluto.ini`). +The data directory is the found automatically, as well as the grid geometry. +The formats are searched in the order (dbl, flt, vtk, dbl.h5, flt.h5) and the first found loaded, this can be overriden. +```python +sim = pp.Simulation("/path/to/simulation", format="flt") +``` +The simulation object provides access to all outputs (of this format), the grid and simulation metadata. +A few examples of accesible attributes: +```python +sim.dims # domain resolution +sim.x1, sim.x2, sim.x3 # cell centered coordinates, redirect to sim.grid.x{1,2,3} +sim.x1i, sim.x2i, sim.x3i # cell interface coordinates +sim.Lx1, sim.Lx2, sim.Lx3 -sim = pp.Simulation("path_to_simulation") -print(sim.grid) - -# Access to grid coordinates -sim.x1 -sim.vx1 - -# Access to simulation steps -sim[3].rho - -# time evolution of mean pressure -mean_prs = sim.reduce(lambda D : D.prs.mean()) +sim.t # simulation output times +sim.vars # simulation output variables ``` -## Concepts -`plutoplot` offers three main classes for handling simulation data: - - `Simulation`: for a simulation - - `PlutoData`: for a single simulation data frame - - `Grid`: for the PLUTO domain grid +The data at the specific output steps can be accessed with the `sim[n]` syntax. +This results in a `PlutoData` object, which can be used to access the data: +```python +sim[-1].rho +``` +The data object as well as the data array are generated when needed, and the data arrays are memory mapped, which means only data actually accessed is read from disk. +The names of the data variables can be found with `sim.vars`. -For data loading the user only has to instantiate a `Simulation`, the grid -and the `PlutoData` objects are created from the `Simulation` when needed. -`PlutoData` uses lazy loading for the actual data, which means the data is -loaded when is first needed, not on object instantiation. -Each variable is loaded seperately (independent of PLUTO save format), -e.g. when only density is needed, pressure is never put into memory. +Be aware that data arrays are always 3-dimensional, even if the domain has a resolution of 1 in some directions. +This is for clarity and consistency, so that an axis always has a direct correspondence to its coordinates in the grid. -## Simulation instantiation -A `Simulation` can be instantiated with: +Simulations are iterable: ```python -Simulation(sim_dir='', format=None, coordinates=None) -``` -- `sim_dir`: Simulation directory (directory with `pluto.ini` and `definitions.h`). - plutoplot searchs for the gridfile and simulation data first in `sim_dir`, - then in `sim_dir/data`, and then looks up the data directory in `pluto.ini`. - Default: Current working directory -- `format`: file format of the simulation data, currently supports `dbl`, `flt`, `vtk` - in both `single_file` and `multiple_files` mode. - Default: `dbl`, `flt`, `vtk`, are tried in that order -- `coordinates`: coordinate system of the simulation grid. - Supports `cartesian`, `spherical`, `polar`, `cylindrical`. - Only necessary for projecting the grind into a cartesian system (e.g. for plotting). - Default: Read coordinate system from `definitions.h`, using `cartesian` as fallback - -## Access `pluto.ini` and `definitions.h` -`plutoplot` can load the PLUTO configuration files: +for step in sim: + print("Total mean squared velocity at t={step.t}: ", (step.vx1**2 + step.vx2**2 + step.vx3**2).mean()) +``` +And also provide a `reduce()` function to run over the whole simulation: ```python -sim = Simulation('sim_dir') -sim.ini['section']['option'] -sim.definitions['options'] +prs_mean = sim.reduce(lambda step: step.prs.mean()) ``` -The returned objects for `pluto.ini` (`Pluto_ini`) and `definitions.h` (`Definitions_H`) -are thin wrappers around `OrderedDict`s. +This results in an array containing the output of the supplied function for each step, in the example the mean pressure. -## Data access -The simulation steps can be optained from the `Simulation` object with the subscript syntax: +#### Working with simulation slices +To only look at a part of a simulation we can slice into it. +This can be particularly useful for analyzing and plotting 2D slices of 3D data, as full 3D plotting is not supported yet. +To slice into a simulation the usual slicing syntax on `Simulation.slicer`: ```python -sim = Simulation('sim_dir') -initial = sim[0] -last = sim[-1] +sliced_sim = sim.slicer[:,0,32:64] ``` -It supports the Python conventions for indexing (zero indexed, negative numbers -are handled as `len(sim)-i`) +This sliced simulation object can now be used as the normal simulation object. +The grid and data arrays will automatically return the data for this slice. +(Note: for clarity a 3D slice is always required. The data arrays will still always be 3D, see above). -Which variables are saved by PLUTO are accesible with +#### Plotting +`plutoplot` provides automatic plotting for 1D & 2D simulations. +To plot slices of 3D simulations, first create a simulation slice (section above), then just follow normally. + +The PlutoData object provides a `plot()` function, which will automatically project the data onto a cartesian grid, and annotating the axes and colorbar correctly: ```python -sim.vars -# or -sim[i].vars -# e.g. ['rho', 'vx1', 'vx2', 'vx3', 'prs'] +sim[-1].plot('rho') ``` +![Density plot](docs/docs/img/quick_start_plot_projected.jpg) -The variable names in this list can be then accessed from the `PlutoData` objects: +The projection can also be turned off, an arbitrary options which will be passed to matplotlib can be given: ```python -sim[0].rho -sim[-1].vx1 +sim[-1].plot('rho', projection=False) ``` -The data is then returned as Numpy arrays, and can be used as usual. +![Density plot](docs/docs/img/quick_start_plot_not-projected.jpg) + +If a plot of a custom quantitity is needed, a array instead of a variable name can be given: +``` +step = sim[-1] +step.plot(step.prs / step.rho, label="T") +``` + +In Jupyter Notebooks interactive plotting can be used to step through the simulation steps. +`Simulation.iplot()` has the same interface as `PlutoData.plot()`, but it will show a slider to step through simulation steps: +``` +sim.iplot("rho") +``` +![Interactive plot](docs/docs/img/quick_start_iplot.gif) + +## Testing +The test suite for `plutoplot` can be found in `test/` and is run by Github actions using `tox` and `pytest`. + +The test suite is currently minimal and has low code coverage. It will be expanded in the future to ensure correctness. + +## Contributing +If you have any questions, suggestions or find a bug, feel free to open an [issue](https://github.com/Simske/plutoplot/issues) +or [Pull Request](https://github.com/Simske/plutoplot/pulls), I am happy to accept contributions to make plutoplot better. + +`plutoplot` uses [pre-commit](https://pre-commit.com/) to ensure a consistend code style, please use it when opening a Pull Request. -## Plotting +## License +GPLv3 diff --git a/docs/.gitignore b/docs/.gitignore new file mode 100644 index 0000000..45ddf0a --- /dev/null +++ b/docs/.gitignore @@ -0,0 +1 @@ +site/ diff --git a/docs/docs/data-access.md b/docs/docs/data-access.md new file mode 100644 index 0000000..7a24a51 --- /dev/null +++ b/docs/docs/data-access.md @@ -0,0 +1,66 @@ +# Data Access +After [creating the simulation object](loading.md) all simulation data can be accessed via this object. +Here the different ways to access data are explored. + +If not explicitly specified, all examples assume an simulation object `sim` is available +```python +import plutoplot as pp + +sim = pp.Simulation("path/to/simulation") +``` + + +The data for the individual timesteps is encapsulated in `PlutoData`-object, which the `Simulation`-object will create on demand. +The data arrays for the variables can be accessed from there. + +## Accessing Steps +### Direct access +To get the `PlutoData`-object for a specific step can be accessed using the `[]`-operator or `get()` function like this: +```python +step_data = sim[10] +step_data = sim.get(10, keep=False) +# or direct acces to variables: +sim[10].rho +``` +`get()` also has an additional parameter `keep`, which chooses if the resulting object should be kept im memory after use. +??? info "`Simulation.get()` docs" + ::: plutoplot.Simulation.get + +### Iteration and `reduce` +It is also possible to iterate over all (or some steps for processing) +```python +for step_data in sim: + # process data here + +# or for more control over the range +for step_data in sim.iter(start, stop, step): + # process data +``` +??? info "`Simulation.iter()` reference" + ::: plutoplot.Simulation.iter + +If each step should be reduced to into an array of values the `reduce` and `reduce_parallel` helpers can be used. +For example, if the mean density of each step is needed: +```python +mean_rho = sim.reduce(lambda step: step.rho.mean()) +# result: mean_rho.shape == len(sim) +``` +More complex reductions with n-dimensional outputs are also supported. The shape of the output can be either given as an argument, or will be deduced from the first calculation: +```python +column_density = sim.reduce(lambda step: step.rho.sum(axis=2)) +# Result: column_density.shape == (n1, n2) +``` +`reduce_parallel` is equivalent, but will use `multiprocessing` to parallelise this operation. Be aware that because of the overhead of multiprocessing this is not necessarily faster than a serial `reduce()`, especially with an optimized `numpy`-installation. + +??? info "`reduce()` reference" + ::: plutoplot.Simulation.reduce +??? info "`reduce_parallel()` reference" + ::: plutoplot.Simulation.reduce_parallel + + +## Accessing data + +The available data variables of a simulation can be accessed from `simulation.vars` or `plutodata.vars`: +```python + +``` diff --git a/docs/docs/img/quick_start_iplot.gif b/docs/docs/img/quick_start_iplot.gif new file mode 100644 index 0000000..18d383a Binary files /dev/null and b/docs/docs/img/quick_start_iplot.gif differ diff --git a/docs/docs/img/quick_start_plot_not-projected.jpg b/docs/docs/img/quick_start_plot_not-projected.jpg new file mode 100644 index 0000000..2bccdcc Binary files /dev/null and b/docs/docs/img/quick_start_plot_not-projected.jpg differ diff --git a/docs/docs/img/quick_start_plot_projected.jpg b/docs/docs/img/quick_start_plot_projected.jpg new file mode 100644 index 0000000..8ab1c3f Binary files /dev/null and b/docs/docs/img/quick_start_plot_projected.jpg differ diff --git a/docs/docs/index.md b/docs/docs/index.md new file mode 100644 index 0000000..16bbf1a --- /dev/null +++ b/docs/docs/index.md @@ -0,0 +1,26 @@ +# plutoplot - easy and fast loading and plotting of PLUTO output files + +`plutoplot` is a Python package for loading, analyzing and plotting data from the [astrophysical gas dynamics simulation code PLUTO](http://plutocode.ph.unito.it/). +By handling simulations as a whole and loading data only when needed (lazy loading), it is fast and easy to use. + +It features: + +- Loading on data actually needed (by lazy loading in memory mapping) +- easy slicing into large datasets (e.g. plotting 2D slice of 3D dataset) +- plotting non-cartesian coordinates projected into cartesian space +- interactive plotting in Jupyter Notebooks +- CLI tool to quickly acquire information about simulations +- Access to parameters set in `definitions.h` and `pluto.ini` +- Access to simulation metadata and grid properties +- Indexing with `ijk` (like `pyPLUTO`) and `kji` (like PLUTO internally) schemes + +There is currently no support for: + +- Particles +- Adaptive grids (AMR) +- 3D plotting (only plotting 2D slices of 3D data is supported.) + +To get started, check out the [Quick Start Guide](quickstart.md) and the [examples](https://github.com/Simske/plutoplot/tree/main/test). + +f you have any questions, suggestions or find a bug, feel free to open an [issue](https://github.com/Simske/plutoplot/issues) +or [Pull Request](https://github.com/Simske/plutoplot/pulls), I am happy to accept contributions to make plutoplot better. diff --git a/docs/docs/loading.md b/docs/docs/loading.md new file mode 100644 index 0000000..1616252 --- /dev/null +++ b/docs/docs/loading.md @@ -0,0 +1,90 @@ +# Loading simulations +Loading data from simulations is the central function `plutoplot` serves. + +The central object to interact with a PLUTO simulation is the `plutoplot.Simulation` object. +In loads the simulation metadata, the grid and creates the objects for the individual output files. + +## Simulation + +To load a simulation from disk create a `plutoplot.Simulation` object: +```python +import plutoplot as pp + +sim = pp.Simulation("path/to/simulation", format="flt") +``` +Additionally the coordinates system and indexing can be set manually. +If no format is given, the first existing format is used (in the order `dbl`, `flt`, `vtk`, `dbl.h5`, `flt.h5`). + +The coordinate system will be read from the gridfile if not specified. More information on the coordinate system can be found in the [Grid section](#grid). + +??? info "plutoplot.Simulation initialization reference" + ::: plutoplot.Simulation.__init__ + +After loading the `Simulation`-object has the following attributes: + +??? info "`Simulation` attributes" + ::: plutoplot.Simulation + selection: + members: false + rendering: + heading_level: 4 + show_root_toc_entry: false + +To show information about the simulation, just use the string representation: +!!! example + ```python + print(sim) + ``` + ``` + PLUTO Simulation: path: 'path/to/simulation', data directory '$sim_path/.' + Data vars: rho, vx1, vx2, vx3 + Data files: Format `flt`: 2 files, last time 1.0, data timestep 1.00e+00 + PLUTO Grid Dimensions: (128, 1, 384), spherical coordinate system + r: 0.40..2.50, Lx1=2.10, N1=128 + theta: 1.45..1.57, Lx1=0.12, N1=1 + phi: 0.00..6.28, Lx1=6.28, N1=384 + ``` + or use the Jupyter Notebook formatting + ```python + sim + ``` + > **PLUTO Simulation** path: `/home/simeon/masterproject/PLUTO/test-problems/HD/Disk_Planet/03_0`, data directory `$sim_path/.` + > Data vars: `rho` `vx1` `vx2` `vx3` + > Data files: Format `flt`: 2 files,last time 1.0, data timestep 1.00e+00 + > **PLUTO Grid** Dimensions (128, 1, 384), spherical coordinate system + > + > | | | | L | N | + > |---|---|---|---|---| + > |$r$|0.40|2.50|2.10|128| + > |$\theta$|1.45|1.57|0.12|1| + > |$\phi$|0.00|6.28|6.28|384| + + +## Slicing simulations + +## Accessing simulation steps +Each simulation output step is represented by a `PlutoData` object, which will be generated on demand by the `Simulation`. The `PlutoData`-object then gives access to the actual data arrays. +The data from the simulation output steps can be accessed from the `Simulation`-object with: + +- direct access using the `[]`-operator or `get()` functions +```python +step_data = sim[10] +step_data = sim.get(10, keep=False) +``` +- iteration +```python +for step in sim: + # process data +``` +- reduced data with `reduce()` and `reduce_parallel()` (over each time step) +```python +mean_density = sim.reduce(lambda step: step.rho.mean()) +``` + +More details in [Data Access](data-access.md) + +## Grid +The `Grid` object contains all the information of the simulation grid. + +??? info "`Grid` reference" + ::: plutoplot.Grid diff --git a/docs/docs/metadata.md b/docs/docs/metadata.md new file mode 100644 index 0000000..eae3b1a --- /dev/null +++ b/docs/docs/metadata.md @@ -0,0 +1,59 @@ +# Reading metadata from pluto.ini & definitions.h + +`plutoplot` can read the PLUTO settings files if needed. + +## `pluto.ini` +`Pluto_ini` encapsulates the `pluto.ini` file, which is available from the simulation object (if `pluto.ini` is in the simulation directory). +In Jupyter Notebooks the config will be displayed as a table. +It is also possible to edit `Pluto_ini` and write it back to file. + +!!! warning "Currently all values are strings and have to be converted to their respective datatype for use" + This is subject to change, see [Github Issue](https://github.com/Simske/plutoplot/issues/11) + + +!!! example + - Access from simulation + ```python + sim = pp.Simulation("path/to/simulation") + + sim.ini["Time"]["tstop"] + sim.ini["Time","tstop"] + sim.ini["Time/tstop"] + ``` + + - access directly from file and change values + ```python + ini = pp.Pluto_ini("path/to/pluto.ini") + + ini["Time/tstop"] = "2.0" + ini.write("path/to/pluto.ini") + ``` + +??? info "`Pluto_ini` reference" + ::: plutoplot.Pluto_ini + + +## `definitions.h` +`Definitions.h` is available similarly as a `Definitions_h`-object, which is a `OrderedDict`. +It is also available from the `Simulation`-object or can be read from a file. + +The keys are handled case-insensitively for convenience. + +!!! example + ```python + sim = pp.Simulation("path/to/simulation") + + sim.definitions["cooling"] + # output example: NO + ``` + or + ```python + defs = pp.Definitions_h("path/to/definitions.h") + + defs["physics"] + # output example: HD + ``` +Currently `Definitions_h`-files cannot be edited, see progress on this in [Github Issue](https://github.com/Simske/plutoplot/issues/10). + +??? info "`Definitions_h` reference" + ::: plutoplot.Definitions_h diff --git a/docs/docs/plotting.md b/docs/docs/plotting.md new file mode 100644 index 0000000..e69de29 diff --git a/docs/docs/quickstart.md b/docs/docs/quickstart.md new file mode 100644 index 0000000..68fe3dd --- /dev/null +++ b/docs/docs/quickstart.md @@ -0,0 +1,127 @@ +# Installation +`plutoplot` requires Python >=3.6. Make sure for installation to install in the right environment, and/or adapt the pip commands accordingly (e.g. `pip3`). + +The base version of plutoplot can be installed from Pypi with: +```bash +pip install --upgrade plutoplot +``` + +To keep the installation size small the dependencies for interactive plotting and loading of HDF5 data are declared as optional dependencies. +To install the optional dependencies use either of the following, depeding on your needs: +```bash +pip install --upgrade plutoplot[interactive] +pip install --upgrade plutoplot[hdf5] +pip install --upgrade plutoplot[interactive,hdf5] +``` + +To install the current development version from Github: +```bash +pip install --upgrade "plutoplot @ git+https://github.com/simske/plutoplot" +``` + +# Quick Start +## CLI: check simulation info +To quickly check the status of a PLUTO simulation, you can use the `pluto-info` command line tool: +```bash +pluto-info /path/to/simulation +``` +Sample output: +``` +>> pluto-info test-problems/HD/Jet/01/ +PLUTO simulation at 'test-problems/HD/Jet/01' +Polar grid with dimensions (160, 1, 640) +Domain: x1: 0.00e+00 .. 1.00e+01 (Lx1 = 1.00e+01) + x2: 0.00e+00 .. 1.00e+00 (Lx2 = 1.00e+00) + x2: 0.00e+00 .. 4.00e+01 (Lx3 = 4.00e+01) +Available variables: rho vx1 vx2 vx3 prs +Data files: + Format dbl: 16 files, last time 15.0, data timestep 1.00e+00 + Format flt: 61 files, last time 15.0, data timestep 2.50e-01 + +``` +(note: depending on your Python environment, the entrypoint `pluto-info` might not be installed correctly. Check the [documentation for more details](https://plutoplot.readthedocs.io/en/latest/cli-tools)). + +## Quick start in Python scripts / Jupyter notebooks +```python +import plutoplot as pp +``` +### Basics +Simulations can be loaded by just providing the path to the simulation directory (directory with `definitions.h` and `pluto.ini`). +The data directory is the found automatically, as well as the grid geometry. +The formats are searched in the order (dbl, flt, vtk, dbl.h5, flt.h5) and the first found loaded, this can be overriden. +```python +sim = pp.Simulation("/path/to/simulation", format="flt") +``` +The simulation object provides access to all outputs (of this format), the grid and simulation metadata. +A few examples of accesible attributes: +```python +sim.dims # domain resolution +sim.x1, sim.x2, sim.x3 # cell centered coordinates, redirect to sim.grid.x{1,2,3} +sim.x1i, sim.x2i, sim.x3i # cell interface coordinates +sim.Lx1, sim.Lx2, sim.Lx3 + +sim.t # simulation output times +sim.vars # simulation output variables +``` + +The data at the specific output steps can be accessed with the `sim[n]` syntax. +This results in a `PlutoData` object, which can be used to access the data: +```python +sim[-1].rho +``` +The data object as well as the data array are generated when needed, and the data arrays are memory mapped, which means only data actually accessed is read from disk. +The names of the data variables can be found with `sim.vars`. + +Be aware that data arrays are always 3-dimensional, even if the domain has a resolution of 1 in some directions. +This is for clarity and consistency, so that an axis always has a direct correspondence to its coordinates in the grid. + +Simulations are iterable: +```python +for step in sim: + print("Total mean squared velocity at t={step.t}: ", (step.vx1**2 + step.vx2**2 + step.vx3**2).mean()) +``` +And also provide a `reduce()` function to run over the whole simulation: +```python +prs_mean = sim.reduce(lambda step: step.prs.mean()) +``` +This results in an array containing the output of the supplied function for each step, in the example the mean pressure. + +### Working with simulation slices +To only look at a part of a simulation we can slice into it. +This can be particularly useful for analyzing and plotting 2D slices of 3D data, as full 3D plotting is not supported yet. +To slice into a simulation the usual slicing syntax on `Simulation.slicer`: +```python +sliced_sim = sim.slicer[:,0,32:64] +``` +This sliced simulation object can now be used as the normal simulation object. +The grid and data arrays will automatically return the data for this slice. +(Note: for clarity a 3D slice is always required. The data arrays will still always be 3D, see above). + +### Plotting +`plutoplot` provides automatic plotting for 1D & 2D simulations. +To plot slices of 3D simulations, first create a simulation slice (section above), then just follow normally. + +The PlutoData object provides a `plot()` function, which will automatically project the data onto a cartesian grid, and annotating the axes and colorbar correctly: +```python +sim[-1].plot('rho') +``` +![Density plot](img/quick_start_plot_projected.jpg) + +The projection can also be turned off, an arbitrary options which will be passed to matplotlib can be given: +```python +sim[-1].plot('rho', projection=False) +``` +![Density plot](img/quick_start_plot_not-projected.jpg) + +If a plot of a custom quantitity is needed, a array instead of a variable name can be given: +``` +step = sim[-1] +step.plot(step.prs / step.rho, label="T") +``` + +In Jupyter Notebooks interactive plotting can be used to step through the simulation steps. +`Simulation.iplot()` has the same interface as `PlutoData.plot()`, but it will show a slider to step through simulation steps: +``` +sim.iplot("rho") +``` +![Interactive plot](img/quick_start_iplot.gif) diff --git a/docs/generate_plots.py b/docs/generate_plots.py new file mode 100644 index 0000000..ef3a67a --- /dev/null +++ b/docs/generate_plots.py @@ -0,0 +1,26 @@ +#!/usr/bin/env python3 +""" +Script to generate sample plots for documentation from PLUTO test problems +""" +import os +from pathlib import Path + +import plutoplot as pp + +base_path = Path(os.getenv("PLUTO_TEST_PROBLEMS")) +dest_path = Path("docs/img") + +# Plots for quick start +sim = pp.Simulation( + "/home/simeon/masterproject/PLUTO/test-problems/HD/Disk_Planet/03_0", format="flt" +) +fig, _ = sim.plot("rho") +fig.savefig(dest_path / "quick_start_plot_projected.jpg", bbox_inches="tight", dpi=75) + +fig, _ = sim.plot("rho", projection=False) +fig.savefig( + dest_path / "quick_start_plot_not-projected.jpg", bbox_inches="tight", dpi=75 +) + + +print("Plots generated") diff --git a/docs/javascripts/mathjax.js b/docs/javascripts/mathjax.js new file mode 100644 index 0000000..117b046 --- /dev/null +++ b/docs/javascripts/mathjax.js @@ -0,0 +1,16 @@ +window.MathJax = { + tex: { + inlineMath: [["\\(", "\\)"]], + displayMath: [["\\[", "\\]"]], + processEscapes: true, + processEnvironments: true, + }, + options: { + ignoreHtmlClass: ".*|", + processHtmlClass: "arithmatex", + }, +}; + +document$.subscribe(() => { + MathJax.typesetPromise(); +}); diff --git a/docs/mkdocs.yml b/docs/mkdocs.yml new file mode 100644 index 0000000..62d0122 --- /dev/null +++ b/docs/mkdocs.yml @@ -0,0 +1,37 @@ +site_name: plutoplot Documentation + +nav: + - Home: index.md + - Quick Start: quickstart.md + - Loading Simulations: loading.md + - Data Access: data-access.md + - Accessing pluto.ini & definitions.h: metadata.md + - Plotting: plotting.md + +theme: + name: material + +markdown_extensions: + - admonition + - pymdownx.details + - pymdownx.superfences + - pymdownx.arithmatex: + generic: true + +plugins: + - search + - mkdocstrings: + default_handler: python + handlers: + python: + rendering: + show_source: false + show_root_heading: true + heading_level: 3 + watch: + - ../plutoplot + +extra_javascript: + - javascripts/mathjax.js + - https://polyfill.io/v3/polyfill.min.js?features=es6 + - https://cdn.jsdelivr.net/npm/mathjax@3/es5/tex-mml-chtml.js diff --git a/docs/requirements.txt b/docs/requirements.txt new file mode 100644 index 0000000..92d95ff --- /dev/null +++ b/docs/requirements.txt @@ -0,0 +1,4 @@ +mkdocs>=1.2 +mkdocs-material>=7.3 +mkdocstrings>=0.16 +pymdown-extensions diff --git a/plutoplot/__init__.py b/plutoplot/__init__.py index d27717b..bc6818b 100644 --- a/plutoplot/__init__.py +++ b/plutoplot/__init__.py @@ -1,10 +1,10 @@ -from ._version import get_versions +import importlib.metadata -__version__ = get_versions()["version"] -del get_versions - -from matplotlib.pyplot import show +__version__ = importlib.metadata.version("plutoplot") +del importlib from . import misc +from .grid import Grid +from .metadata import Definitions_h, Pluto_ini from .plutodata import PlutoData from .simulation import Simulation diff --git a/plutoplot/_version.py b/plutoplot/_version.py deleted file mode 100644 index 98f27ac..0000000 --- a/plutoplot/_version.py +++ /dev/null @@ -1,556 +0,0 @@ -# This file helps to compute a version number in source trees obtained from -# git-archive tarball (such as those provided by githubs download-from-tag -# feature). Distribution tarballs (built by setup.py sdist) and build -# directories (produced by setup.py build) will contain a much shorter file -# that just contains the computed version number. - -# This file is released into the public domain. Generated by -# versioneer-0.18 (https://github.com/warner/python-versioneer) - -"""Git implementation of _version.py.""" - -import errno -import os -import re -import subprocess -import sys - - -def get_keywords(): - """Get the keywords needed to look up the version information.""" - # these strings will be replaced by git during git-archive. - # setup.py/versioneer.py will grep for the variable names, so they must - # each be defined on a line of their own. _version.py will just call - # get_keywords(). - git_refnames = "$Format:%d$" - git_full = "$Format:%H$" - git_date = "$Format:%ci$" - keywords = {"refnames": git_refnames, "full": git_full, "date": git_date} - return keywords - - -class VersioneerConfig: - """Container for Versioneer configuration parameters.""" - - -def get_config(): - """Create, populate and return the VersioneerConfig() object.""" - # these strings are filled in when 'setup.py versioneer' creates - # _version.py - cfg = VersioneerConfig() - cfg.VCS = "git" - cfg.style = "pep440" - cfg.tag_prefix = "" - cfg.parentdir_prefix = "" - cfg.versionfile_source = "plutoplot/_version.py" - cfg.verbose = False - return cfg - - -class NotThisMethod(Exception): - """Exception raised if a method is not valid for the current scenario.""" - - -LONG_VERSION_PY = {} -HANDLERS = {} - - -def register_vcs_handler(vcs, method): # decorator - """Decorator to mark a method as the handler for a particular VCS.""" - - def decorate(f): - """Store f in HANDLERS[vcs][method].""" - if vcs not in HANDLERS: - HANDLERS[vcs] = {} - HANDLERS[vcs][method] = f - return f - - return decorate - - -def run_command(commands, args, cwd=None, verbose=False, hide_stderr=False, env=None): - """Call the given command(s).""" - assert isinstance(commands, list) - p = None - for c in commands: - try: - dispcmd = str([c] + args) - # remember shell=False, so use git.cmd on windows, not just git - p = subprocess.Popen( - [c] + args, - cwd=cwd, - env=env, - stdout=subprocess.PIPE, - stderr=(subprocess.PIPE if hide_stderr else None), - ) - break - except EnvironmentError: - e = sys.exc_info()[1] - if e.errno == errno.ENOENT: - continue - if verbose: - print("unable to run %s" % dispcmd) - print(e) - return None, None - else: - if verbose: - print("unable to find command, tried %s" % (commands,)) - return None, None - stdout = p.communicate()[0].strip() - if sys.version_info[0] >= 3: - stdout = stdout.decode() - if p.returncode != 0: - if verbose: - print("unable to run %s (error)" % dispcmd) - print("stdout was %s" % stdout) - return None, p.returncode - return stdout, p.returncode - - -def versions_from_parentdir(parentdir_prefix, root, verbose): - """Try to determine the version from the parent directory name. - - Source tarballs conventionally unpack into a directory that includes both - the project name and a version string. We will also support searching up - two directory levels for an appropriately named parent directory - """ - rootdirs = [] - - for i in range(3): - dirname = os.path.basename(root) - if dirname.startswith(parentdir_prefix): - return { - "version": dirname[len(parentdir_prefix) :], - "full-revisionid": None, - "dirty": False, - "error": None, - "date": None, - } - else: - rootdirs.append(root) - root = os.path.dirname(root) # up a level - - if verbose: - print( - "Tried directories %s but none started with prefix %s" - % (str(rootdirs), parentdir_prefix) - ) - raise NotThisMethod("rootdir doesn't start with parentdir_prefix") - - -@register_vcs_handler("git", "get_keywords") -def git_get_keywords(versionfile_abs): - """Extract version information from the given file.""" - # the code embedded in _version.py can just fetch the value of these - # keywords. When used from setup.py, we don't want to import _version.py, - # so we do it with a regexp instead. This function is not used from - # _version.py. - keywords = {} - try: - f = open(versionfile_abs, "r") - for line in f.readlines(): - if line.strip().startswith("git_refnames ="): - mo = re.search(r'=\s*"(.*)"', line) - if mo: - keywords["refnames"] = mo.group(1) - if line.strip().startswith("git_full ="): - mo = re.search(r'=\s*"(.*)"', line) - if mo: - keywords["full"] = mo.group(1) - if line.strip().startswith("git_date ="): - mo = re.search(r'=\s*"(.*)"', line) - if mo: - keywords["date"] = mo.group(1) - f.close() - except EnvironmentError: - pass - return keywords - - -@register_vcs_handler("git", "keywords") -def git_versions_from_keywords(keywords, tag_prefix, verbose): - """Get version information from git keywords.""" - if not keywords: - raise NotThisMethod("no keywords at all, weird") - date = keywords.get("date") - if date is not None: - # git-2.2.0 added "%cI", which expands to an ISO-8601 -compliant - # datestamp. However we prefer "%ci" (which expands to an "ISO-8601 - # -like" string, which we must then edit to make compliant), because - # it's been around since git-1.5.3, and it's too difficult to - # discover which version we're using, or to work around using an - # older one. - date = date.strip().replace(" ", "T", 1).replace(" ", "", 1) - refnames = keywords["refnames"].strip() - if refnames.startswith("$Format"): - if verbose: - print("keywords are unexpanded, not using") - raise NotThisMethod("unexpanded keywords, not a git-archive tarball") - refs = set([r.strip() for r in refnames.strip("()").split(",")]) - # starting in git-1.8.3, tags are listed as "tag: foo-1.0" instead of - # just "foo-1.0". If we see a "tag: " prefix, prefer those. - TAG = "tag: " - tags = set([r[len(TAG) :] for r in refs if r.startswith(TAG)]) - if not tags: - # Either we're using git < 1.8.3, or there really are no tags. We use - # a heuristic: assume all version tags have a digit. The old git %d - # expansion behaves like git log --decorate=short and strips out the - # refs/heads/ and refs/tags/ prefixes that would let us distinguish - # between branches and tags. By ignoring refnames without digits, we - # filter out many common branch names like "release" and - # "stabilization", as well as "HEAD" and "master". - tags = set([r for r in refs if re.search(r"\d", r)]) - if verbose: - print("discarding '%s', no digits" % ",".join(refs - tags)) - if verbose: - print("likely tags: %s" % ",".join(sorted(tags))) - for ref in sorted(tags): - # sorting will prefer e.g. "2.0" over "2.0rc1" - if ref.startswith(tag_prefix): - r = ref[len(tag_prefix) :] - if verbose: - print("picking %s" % r) - return { - "version": r, - "full-revisionid": keywords["full"].strip(), - "dirty": False, - "error": None, - "date": date, - } - # no suitable tags, so version is "0+unknown", but full hex is still there - if verbose: - print("no suitable tags, using unknown + full revision id") - return { - "version": "0+unknown", - "full-revisionid": keywords["full"].strip(), - "dirty": False, - "error": "no suitable tags", - "date": None, - } - - -@register_vcs_handler("git", "pieces_from_vcs") -def git_pieces_from_vcs(tag_prefix, root, verbose, run_command=run_command): - """Get version from 'git describe' in the root of the source tree. - - This only gets called if the git-archive 'subst' keywords were *not* - expanded, and _version.py hasn't already been rewritten with a short - version string, meaning we're inside a checked out source tree. - """ - GITS = ["git"] - if sys.platform == "win32": - GITS = ["git.cmd", "git.exe"] - - out, rc = run_command(GITS, ["rev-parse", "--git-dir"], cwd=root, hide_stderr=True) - if rc != 0: - if verbose: - print("Directory %s not under git control" % root) - raise NotThisMethod("'git rev-parse --git-dir' returned error") - - # if there is a tag matching tag_prefix, this yields TAG-NUM-gHEX[-dirty] - # if there isn't one, this yields HEX[-dirty] (no NUM) - describe_out, rc = run_command( - GITS, - [ - "describe", - "--tags", - "--dirty", - "--always", - "--long", - "--match", - "%s*" % tag_prefix, - ], - cwd=root, - ) - # --long was added in git-1.5.5 - if describe_out is None: - raise NotThisMethod("'git describe' failed") - describe_out = describe_out.strip() - full_out, rc = run_command(GITS, ["rev-parse", "HEAD"], cwd=root) - if full_out is None: - raise NotThisMethod("'git rev-parse' failed") - full_out = full_out.strip() - - pieces = {} - pieces["long"] = full_out - pieces["short"] = full_out[:7] # maybe improved later - pieces["error"] = None - - # parse describe_out. It will be like TAG-NUM-gHEX[-dirty] or HEX[-dirty] - # TAG might have hyphens. - git_describe = describe_out - - # look for -dirty suffix - dirty = git_describe.endswith("-dirty") - pieces["dirty"] = dirty - if dirty: - git_describe = git_describe[: git_describe.rindex("-dirty")] - - # now we have TAG-NUM-gHEX or HEX - - if "-" in git_describe: - # TAG-NUM-gHEX - mo = re.search(r"^(.+)-(\d+)-g([0-9a-f]+)$", git_describe) - if not mo: - # unparseable. Maybe git-describe is misbehaving? - pieces["error"] = "unable to parse git-describe output: '%s'" % describe_out - return pieces - - # tag - full_tag = mo.group(1) - if not full_tag.startswith(tag_prefix): - if verbose: - fmt = "tag '%s' doesn't start with prefix '%s'" - print(fmt % (full_tag, tag_prefix)) - pieces["error"] = "tag '%s' doesn't start with prefix '%s'" % ( - full_tag, - tag_prefix, - ) - return pieces - pieces["closest-tag"] = full_tag[len(tag_prefix) :] - - # distance: number of commits since tag - pieces["distance"] = int(mo.group(2)) - - # commit: short hex revision ID - pieces["short"] = mo.group(3) - - else: - # HEX: no tags - pieces["closest-tag"] = None - count_out, rc = run_command(GITS, ["rev-list", "HEAD", "--count"], cwd=root) - pieces["distance"] = int(count_out) # total number of commits - - # commit date: see ISO-8601 comment in git_versions_from_keywords() - date = run_command(GITS, ["show", "-s", "--format=%ci", "HEAD"], cwd=root)[ - 0 - ].strip() - pieces["date"] = date.strip().replace(" ", "T", 1).replace(" ", "", 1) - - return pieces - - -def plus_or_dot(pieces): - """Return a + if we don't already have one, else return a .""" - if "+" in pieces.get("closest-tag", ""): - return "." - return "+" - - -def render_pep440(pieces): - """Build up version string, with post-release "local version identifier". - - Our goal: TAG[+DISTANCE.gHEX[.dirty]] . Note that if you - get a tagged build and then dirty it, you'll get TAG+0.gHEX.dirty - - Exceptions: - 1: no tags. git_describe was just HEX. 0+untagged.DISTANCE.gHEX[.dirty] - """ - if pieces["closest-tag"]: - rendered = pieces["closest-tag"] - if pieces["distance"] or pieces["dirty"]: - rendered += plus_or_dot(pieces) - rendered += "%d.g%s" % (pieces["distance"], pieces["short"]) - if pieces["dirty"]: - rendered += ".dirty" - else: - # exception #1 - rendered = "0+untagged.%d.g%s" % (pieces["distance"], pieces["short"]) - if pieces["dirty"]: - rendered += ".dirty" - return rendered - - -def render_pep440_pre(pieces): - """TAG[.post.devDISTANCE] -- No -dirty. - - Exceptions: - 1: no tags. 0.post.devDISTANCE - """ - if pieces["closest-tag"]: - rendered = pieces["closest-tag"] - if pieces["distance"]: - rendered += ".post.dev%d" % pieces["distance"] - else: - # exception #1 - rendered = "0.post.dev%d" % pieces["distance"] - return rendered - - -def render_pep440_post(pieces): - """TAG[.postDISTANCE[.dev0]+gHEX] . - - The ".dev0" means dirty. Note that .dev0 sorts backwards - (a dirty tree will appear "older" than the corresponding clean one), - but you shouldn't be releasing software with -dirty anyways. - - Exceptions: - 1: no tags. 0.postDISTANCE[.dev0] - """ - if pieces["closest-tag"]: - rendered = pieces["closest-tag"] - if pieces["distance"] or pieces["dirty"]: - rendered += ".post%d" % pieces["distance"] - if pieces["dirty"]: - rendered += ".dev0" - rendered += plus_or_dot(pieces) - rendered += "g%s" % pieces["short"] - else: - # exception #1 - rendered = "0.post%d" % pieces["distance"] - if pieces["dirty"]: - rendered += ".dev0" - rendered += "+g%s" % pieces["short"] - return rendered - - -def render_pep440_old(pieces): - """TAG[.postDISTANCE[.dev0]] . - - The ".dev0" means dirty. - - Eexceptions: - 1: no tags. 0.postDISTANCE[.dev0] - """ - if pieces["closest-tag"]: - rendered = pieces["closest-tag"] - if pieces["distance"] or pieces["dirty"]: - rendered += ".post%d" % pieces["distance"] - if pieces["dirty"]: - rendered += ".dev0" - else: - # exception #1 - rendered = "0.post%d" % pieces["distance"] - if pieces["dirty"]: - rendered += ".dev0" - return rendered - - -def render_git_describe(pieces): - """TAG[-DISTANCE-gHEX][-dirty]. - - Like 'git describe --tags --dirty --always'. - - Exceptions: - 1: no tags. HEX[-dirty] (note: no 'g' prefix) - """ - if pieces["closest-tag"]: - rendered = pieces["closest-tag"] - if pieces["distance"]: - rendered += "-%d-g%s" % (pieces["distance"], pieces["short"]) - else: - # exception #1 - rendered = pieces["short"] - if pieces["dirty"]: - rendered += "-dirty" - return rendered - - -def render_git_describe_long(pieces): - """TAG-DISTANCE-gHEX[-dirty]. - - Like 'git describe --tags --dirty --always -long'. - The distance/hash is unconditional. - - Exceptions: - 1: no tags. HEX[-dirty] (note: no 'g' prefix) - """ - if pieces["closest-tag"]: - rendered = pieces["closest-tag"] - rendered += "-%d-g%s" % (pieces["distance"], pieces["short"]) - else: - # exception #1 - rendered = pieces["short"] - if pieces["dirty"]: - rendered += "-dirty" - return rendered - - -def render(pieces, style): - """Render the given version pieces into the requested style.""" - if pieces["error"]: - return { - "version": "unknown", - "full-revisionid": pieces.get("long"), - "dirty": None, - "error": pieces["error"], - "date": None, - } - - if not style or style == "default": - style = "pep440" # the default - - if style == "pep440": - rendered = render_pep440(pieces) - elif style == "pep440-pre": - rendered = render_pep440_pre(pieces) - elif style == "pep440-post": - rendered = render_pep440_post(pieces) - elif style == "pep440-old": - rendered = render_pep440_old(pieces) - elif style == "git-describe": - rendered = render_git_describe(pieces) - elif style == "git-describe-long": - rendered = render_git_describe_long(pieces) - else: - raise ValueError("unknown style '%s'" % style) - - return { - "version": rendered, - "full-revisionid": pieces["long"], - "dirty": pieces["dirty"], - "error": None, - "date": pieces.get("date"), - } - - -def get_versions(): - """Get version information or return default if unable to do so.""" - # I am in _version.py, which lives at ROOT/VERSIONFILE_SOURCE. If we have - # __file__, we can work backwards from there to the root. Some - # py2exe/bbfreeze/non-CPython implementations don't do __file__, in which - # case we can only use expanded keywords. - - cfg = get_config() - verbose = cfg.verbose - - try: - return git_versions_from_keywords(get_keywords(), cfg.tag_prefix, verbose) - except NotThisMethod: - pass - - try: - root = os.path.realpath(__file__) - # versionfile_source is the relative path from the top of the source - # tree (where the .git directory might live) to this file. Invert - # this to find the root from __file__. - for i in cfg.versionfile_source.split("/"): - root = os.path.dirname(root) - except NameError: - return { - "version": "0+unknown", - "full-revisionid": None, - "dirty": None, - "error": "unable to find root of source tree", - "date": None, - } - - try: - pieces = git_pieces_from_vcs(cfg.tag_prefix, root, verbose) - return render(pieces, cfg.style) - except NotThisMethod: - pass - - try: - if cfg.parentdir_prefix: - return versions_from_parentdir(cfg.parentdir_prefix, root, verbose) - except NotThisMethod: - pass - - return { - "version": "0+unknown", - "full-revisionid": None, - "dirty": None, - "error": "unable to compute version", - "date": None, - } diff --git a/plutoplot/coordinates.py b/plutoplot/coordinates.py index 229226b..bb728f3 100644 --- a/plutoplot/coordinates.py +++ b/plutoplot/coordinates.py @@ -1,9 +1,12 @@ """Functions and mappings for coordinate grid""" from functools import lru_cache -from typing import Dict +from typing import TYPE_CHECKING, Dict, Tuple import numpy as np +if TYPE_CHECKING: + from .grid import Grid + base_coordinate_mappings: Dict[str, Dict[str, str]] = { "cartesian": {"x": "x1", "y": "x2", "z": "x3"}, "polar": {"r": "x1", "phi": "x2", "z": "x3"}, @@ -12,7 +15,7 @@ } -@lru_cache +@lru_cache() def mapping_grid(coordinates: str) -> Dict[str, str]: """Generate variable name mapping for specified coordinate system. @@ -38,7 +41,7 @@ def mapping_grid(coordinates: str) -> Dict[str, str]: return mapping -@lru_cache +@lru_cache() def mapping_vars(coordinates: str) -> Dict[str, str]: """Coordinate name mapping for velocity components @@ -67,7 +70,7 @@ def mapping_vars(coordinates: str) -> Dict[str, str]: return mapping -tex_chars = { +tex_chars: Dict[str, str] = { "theta": r"\theta", "rho": r"\rho", "phi": r"\phi", @@ -78,7 +81,7 @@ def mapping_vars(coordinates: str) -> Dict[str, str]: } -@lru_cache +@lru_cache() def mapping_tex(coordinates: str) -> Dict[str, str]: """Coordinate and variable mapping to LaTeX math mode symbols. @@ -122,31 +125,43 @@ def mapping_tex(coordinates: str) -> Dict[str, str]: return mapping -def transform_mesh(grid, mesh1, mesh2): +def transform_mesh( + grid: "Grid", + mesh1: np.ndarray[np.dtype[np.float64], np.dtype[np.float64]], + mesh2: np.ndarray[np.dtype[np.float64], np.dtype[np.float64]], +) -> Tuple[ + Tuple[str, str], + Tuple[ + np.ndarray[np.dtype[np.float64], np.dtype[np.float64]], + np.ndarray[np.dtype[np.float64], np.dtype[np.float64]], + ], +]: if grid.coordinates == "cartesian": - return ( + names = ( f"{grid.mapping_tex[f'x{grid.rdims_ind[0]+1}']}", f"{grid.mapping_tex[f'x{grid.rdims_ind[1]+1}']}", - ), (mesh1, mesh2) + ) + meshes = mesh1, mesh2 elif grid.coordinates == "spherical": if grid.rdims_ind == (0, 1): r = mesh1 z = r * np.cos(mesh2) - return ("r", "z"), (r, z) + names, meshes = ("r", "z"), (r, z) elif grid.rdims_ind == (0, 2): factor = mesh1 * np.sin(grid.x2[0]) x = factor * np.cos(mesh2) y = factor * np.sin(mesh2) - return ("x", "y"), (x, y) + names, meshes = ("x", "y"), (x, y) raise NotImplementedError("Projection in (theta, phi) not supported") elif grid.coordinates == "cylindrical": - return ("r", "z"), (mesh1, mesh2) + names, meshes = ("r", "z"), (mesh1, mesh2) elif grid.coordinates == "polar": if grid.rdims_ind == (0, 1): x = mesh1 * np.cos(mesh2) - y = mesh2 * np.sin(mesh2) - return ("x", "y"), (x, y) + y = mesh1 * np.sin(mesh2) + names, meshes = ("x", "y"), (x, y) elif grid.rdims_ind == (0, 2): - return ("r", "z"), (mesh1, mesh2) + names, meshes = ("r", "z"), (mesh1, mesh2) else: raise NotImplementedError("Projection in (phi, z) not supported") + return names, meshes diff --git a/plutoplot/grid.py b/plutoplot/grid.py index fa628f3..7d4b87b 100644 --- a/plutoplot/grid.py +++ b/plutoplot/grid.py @@ -1,5 +1,5 @@ from pathlib import Path -from typing import Dict +from typing import Dict, Optional, List, Tuple import numpy as np @@ -45,7 +45,9 @@ class Grid: * Generalize and document meshgrid functions """ - def __init__(self, gridfile: Path, coordinates: str = None, indexing="ijk"): + def __init__( + self, gridfile: Path, coordinates: Optional[str] = None, indexing: str = "ijk" + ): """Initialize Grid from gridfile Args: @@ -55,10 +57,10 @@ def __init__(self, gridfile: Path, coordinates: str = None, indexing="ijk"): indexing (:obj:`str`, optional): index order for arrays. 'ijk' or 'kji' """ self.gridfile_path: Path = Path(gridfile) - self.coordinates: str = None - self.mapping_grid: Dict[str, str] = None - self.mapping_vars: Dict[str, str] = None - self.mapping_tex: Dict[str, str] = None + self.coordinates: Optional[str] = None + self.mapping_grid: Dict[str, str] = {} + self.mapping_vars: Dict[str, str] = {} + self.mapping_tex: Dict[str, str] = {} # helper function to transpose arrays if necessary if indexing == "ijk": @@ -90,7 +92,9 @@ def set_coordinate_system(self, coordinates: str) -> None: self.mapping_vars = mapping_vars(coordinates) self.mapping_tex = mapping_tex(coordinates) - def read_gridfile(self, gridfile_path: Path, coordinates: str = None) -> None: + def read_gridfile( + self, gridfile_path: Path, coordinates: Optional[str] = None + ) -> None: """Read and parse gridfile Args: @@ -110,7 +114,7 @@ def read_gridfile(self, gridfile_path: Path, coordinates: str = None) -> None: """ # to be filled with left and right cell interfaces x = [] - dims = [] + dims: List[int] = [] with gridfile_path.open() as gf: # Gridfile header header = False # marker if gf pointer is in header @@ -166,15 +170,17 @@ def read_gridfile(self, gridfile_path: Path, coordinates: str = None) -> None: self.data_shape = tuple(reversed(dims)) if self.indexing == "ijk": + self.shape = self.dims self.rmask = tuple(slice(None) if dim > 1 else 0 for dim in self.dims) else: + self.shape = tuple(reversed(self.dims)) self.rmask = tuple(slice(None) if dim > 1 else 0 for dim in self.data_shape) self.size = np.product(self.dims) @cached_property def mesh_center(self): - """ + """n.dohrmann1300@gmail.com 2D cell center mesh in native coordinates Returns: X, Y with shape for each: (dim[1],dim[0]) @@ -230,8 +236,12 @@ def __getattr__(self, name: str): raise AttributeError(f"{type(self).__name__} has no attribute '{name}'") def __str__(self) -> str: + mapping_inv = {value: key for key, value in self.mapping_grid.items()} return ( - f"PLUTO Grid, Dimensions {self.dims}, Coordinate System: {self.coordinates}" + f"PLUTO Grid Dimensions: {self.dims}, {self.coordinates} coordinate system\n" + f"{mapping_inv['x1']}: {self.x1i[0]:.2f}..{self.x1i[-1]:.2f}, Lx1={self.Lx1:.2f}, N1={self.dims[0]}\n" + f"{mapping_inv['x2']}: {self.x2i[0]:.2f}..{self.x2i[-1]:.2f}, Lx1={self.Lx2:.2f}, N1={self.dims[1]}\n" + f"{mapping_inv['x3']}: {self.x3i[0]:.2f}..{self.x3i[-1]:.2f}, Lx1={self.Lx3:.2f}, N1={self.dims[2]}\n" ) def __repr__(self) -> str: @@ -254,9 +264,7 @@ def __dir__(self): class GridSlice(Grid): def __init__(self, grid: Grid, slice_): - self.slice = tuple( - s if isinstance(s, slice) else slice(s, s + 1) for s in slice_ - ) + self.slice = normalize_slice(slice_, grid.shape) self.slicer = None self.gridfile_path = None @@ -265,17 +273,14 @@ def __init__(self, grid: Grid, slice_): self.T = grid.T self.indexing = grid.indexing - sl_ind = (lambda i: i) if self.indexing == "ijk" else (lambda i: 2 - i) - self.xn = tuple(x[self.slice[sl_ind(i)]] for i, x in enumerate(grid.xn)) - self.xni = [] - for i in range(3): - stop = self.slice[sl_ind(i)].stop - step = self.slice[sl_ind(i)].step - if stop is not None: - stop += 1 if step is None else step - self.xni.append(grid.xni[i][self.slice[sl_ind(i)].start : stop : step]) + # reverse slice depending on indexing + slice_ijk = reversed(self.slice) if self.indexing == "kji" else self.slice - self.xni = tuple(self.xni) + self.xn = tuple(x[sl] for sl, x in zip(slice_ijk, grid.xn)) + self.xni = tuple( + x[sl.start : sl.stop + sl.step : sl.step] + for sl, x in zip(slice_ijk, grid.xni) + ) self.dxn = tuple(x[1:] - x[:-1] for x in self.xni) self.L = tuple(x[-1] - x[0] for x in self.xni) @@ -293,11 +298,66 @@ def __init__(self, grid: Grid, slice_): self.data_shape = None if self.indexing == "ijk": self.rmask = tuple(slice(None) if dim > 1 else 0 for dim in self.dims) + self.shape = self.dims else: self.rmask = tuple( slice(None) if dim > 1 else 0 for dim in reversed(self.dims) ) + self.shape = tuple(reversed(self.dims)) self.size = grid.size # TODO repr and str + + +def normalize_slice(slice_: tuple, shape: tuple) -> tuple: + """Check bounds of 3D slice, and preserve 3d structure of array + for 1-high direction slice + + Args: + slice_ (tuple): 3D slice, consisting of `int` and `slice` + shape (tuple): dimensions of domain + + Returns: + tuple + + Raises: + IndexError: if any of the bounds check don't work + """ + if len(slice_) != 3: + raise IndexError("Please specify 3D slice for clarity") + + newslice = [] + for dimslice, dimsize in zip(slice_, shape): + if isinstance(dimslice, slice): + start, stop, step = dimslice.start, dimslice.stop, dimslice.step + + if start is None: + start = 0 + elif start >= dimsize or start < -dimsize: + raise IndexError("Slice out of bounds") + elif start < 0: + start = dimsize + dimslice.start + + if stop is None: + stop = dimsize + elif stop > dimsize or stop < -dimsize: + raise IndexError("Slice out of bounds") + elif stop < 0: + stop = dimsize + stop + + if step is None: + step = 1 + + newslice.append(slice(start, stop, step)) + + else: + start = dimslice + if start < 0: + start = dimsize + dimslice + if not (0 <= start < dimsize): + raise IndexError("Slice out of bounds") + + newslice.append(slice(start, start + 1, 1)) + + return tuple(newslice) diff --git a/plutoplot/info.py b/plutoplot/info.py index a90cb47..5c24f3f 100644 --- a/plutoplot/info.py +++ b/plutoplot/info.py @@ -34,7 +34,6 @@ def info(simulationpath): sim = sims[0] output = ( f"PLUTO simulation at '{sim.path}'\n" - f"Data directory at '$SIM_DIR/{sim.data_path.relative_to(sim.path)}'\n" f"{sim.grid.coordinates.capitalize()} grid with dimensions {sim.dims}\n" f"Domain: x1: {sim.x1i[0]:.2e} .. {sim.x1i[-1]:.2e} (Lx1 = {sim.Lx1:.2e})\n" f" x2: {sim.x2i[0]:.2e} .. {sim.x2i[-1]:.2e} (Lx2 = {sim.Lx2:.2e})\n" diff --git a/plutoplot/metadata.py b/plutoplot/metadata.py index 953b5cf..2340193 100644 --- a/plutoplot/metadata.py +++ b/plutoplot/metadata.py @@ -260,6 +260,17 @@ def __str__(self) -> str: """Convert to pluto.ini format, with columns aligned inside sections""" return "\n\n".join(str(section) for section in self.sections()) + def _split_key(self, key) -> tuple: + # (section, key) + if isinstance(key, tuple): + return key + sep = key.find("/") + # "section/key" + if sep > -1: + return key[:sep], key[sep + 1 :] + # "section" + return (key,) + def __getitem__(self, key): """ini[key] with multiple syntaxes: @@ -267,23 +278,23 @@ def __getitem__(self, key): - `ini["section","key"] - `ini["section/key"] """ - if isinstance(key, tuple): - return self[key[0]][key[1]] - sep = key.find("/") - if sep > -1: - return self[key[:sep]][key[sep + 1 :]] - return super().__getitem__(key) + key = self._split_key(key) + if len(key) == 2: + return super().__getitem__(key[0])[key[1]] + return super().__getitem__(key[0]) def __setitem__(self, key, value): """ini[key] = value For `key` syntax check `__getitem__()` """ - if isinstance(key, tuple): - self[key[0]][key[1]] = value - sep = key.find("/") - if sep > -1: - self[key[:sep]][key[sep + 1 :]] = value - super().__setitem__(key, value) + key = self._split_key(key) + if len(key) == 1: + super().__setitem__(key[0], value) + else: + if key[0] in self: + self[key[0]][key[1]] = value + else: + super().__setitem__(key[0], self.Section(key[0], {key[1]: value})) def write(self, path: Path = None) -> None: """Write pluto.ini to file. diff --git a/plutoplot/misc.py b/plutoplot/misc.py index d3b697f..7184077 100644 --- a/plutoplot/misc.py +++ b/plutoplot/misc.py @@ -1,21 +1,28 @@ """Miscellaneous tools""" - -def cached_property(func): - """Cache class property decorator - - Caches attribute under `_attr_`. - """ - - def wrapper(self): - cached_name = "_" + func.__name__ - try: +from typing import Dict, Any, Type, Callable, Tuple + +# functools.cached_property exists for Python >=3.8 +# use own implementation for version before +try: + from functools import cached_property +except ImportError: + + def cached_property(func: Callable[[], Any]) -> property: + """Cache class property decorator + + Caches attribute under `_attr_`. + """ + + def wrapper(self) -> Any: + cached_name = "_" + func.__name__ + try: + return getattr(self, cached_name) + except AttributeError: + setattr(self, cached_name, func(self)) return getattr(self, cached_name) - except AttributeError: - setattr(self, cached_name, func(self)) - return getattr(self, cached_name) - return property(wrapper) + return property(wrapper) class Slicer: @@ -26,9 +33,9 @@ class Slicer: slice as additional kwarg (with name `slice_`) to the class. """ - def __init__(self, SliceClass, **kwargs): + def __init__(self, SliceClass: Type[Any], **kwargs: Any) -> None: self.SliceClass = SliceClass self.kwargs = kwargs - def __getitem__(self, slice_): + def __getitem__(self, slice_: Tuple): return self.SliceClass(slice_=slice_, **self.kwargs) diff --git a/plutoplot/plotting.py b/plutoplot/plotting.py index 39210e6..9e3e6ac 100644 --- a/plutoplot/plotting.py +++ b/plutoplot/plotting.py @@ -3,24 +3,29 @@ from matplotlib.ticker import ScalarFormatter from mpl_toolkits.axes_grid1 import make_axes_locatable -from .grid import Grid +from .grid import Grid, GridSlice def plot( data: np.ndarray, grid: Grid, + *, ax=None, label: str = None, figsize=None, cbar=True, - vmin=None, - vmax=None, - cmap=None, projection: bool = True, - **pcolormesh_kwargs, + **mpl_kwargs, ) -> None: """Simple colorplot for 2-dim data""" + if isinstance(grid, GridSlice) and data.shape == grid.shape: + data = data[grid.slice] + elif data.shape == grid.shape: + pass + else: + raise RuntimeError("Plotting: Grid shape not compatible with data") + if len(grid.rdims) == 1: if ax is None: if figsize is None: @@ -31,7 +36,7 @@ def plot( ax.set_ylabel(label) ax.grid() - ax.plot(grid.xn[grid.rdims_ind[0]], data[grid.rmask], label=label) + ax.plot(grid.xn[grid.rdims_ind[0]], data[grid.rmask], label=label, **mpl_kwargs) elif len(grid.rdims) == 2: if projection: @@ -40,7 +45,7 @@ def plot( else: xlabel = f"{grid.mapping_tex[f'x{grid.rdims_ind[0]+1}']}" ylabel = f"{grid.mapping_tex[f'x{grid.rdims_ind[1]+1}']}" - X, Y = grid.xni[grid.rdims_ind[0]], grid.xni[grid.rdims_ind[1]] + X, Y = grid.mesh_edge if ax is None: if figsize is None: @@ -58,17 +63,17 @@ def plot( ax.set_xlabel(f"${xlabel}$") ax.set_ylabel(f"${ylabel}$") - im = ax.pcolormesh( - X, Y, data[grid.rmask], vmin=vmin, vmax=vmax, cmap=cmap, **pcolormesh_kwargs - ) + im = ax.pcolormesh(X, Y, data[grid.rmask], **mpl_kwargs) ax.set_aspect(1) if cbar: formatter = ScalarFormatter() formatter.set_powerlimits((-2, 2)) divider = make_axes_locatable(ax) - cax = divider.append_axes("right", size="10%", pad=0.05) + cax = divider.append_axes("right", size=0.15, pad=0.05) plt.colorbar(im, label=label, format=formatter, cax=cax) + # plt.colorbar(im, label=label, format=formatter, ax=ax, pad=0.05) + elif len(grid.rdims) == 3: raise NotImplementedError("3D plotting not supported (yet)") diff --git a/plutoplot/plutodata.py b/plutoplot/plutodata.py index 58d800b..919284e 100644 --- a/plutoplot/plutodata.py +++ b/plutoplot/plutodata.py @@ -46,9 +46,7 @@ def __init__( self._data = {} self.slicer = Slicer( - lambda slice_: PlutoDataSlice( - self, - ) + lambda slice_: PlutoDataSlice(self, self.grid.slicer[slice_]) ) def __getattr__(self, attr: str): @@ -200,8 +198,6 @@ def plot( self, var: str, grid=None, label: str = None, show_title: bool = True, **kwargs ): """TODO""" - if var is None: - var = self.vars[0] if isinstance(var, str): varname = var var = getattr(self, var) @@ -253,7 +249,7 @@ def __dir__(self) -> list: class PlutoDataSlice(PlutoData): - def __init__(self, parent: PlutoData, *, sliced_grid: Grid = None, slice_=None): + def __init__(self, parent: PlutoData, sliced_grid: Grid = None): self.parent = parent self.n = parent.n self.metadata = parent.metadata @@ -265,20 +261,9 @@ def __init__(self, parent: PlutoData, *, sliced_grid: Grid = None, slice_=None): parent.metadata.nstep[self.n], ) - self.slicer = None + self.grid = sliced_grid - if sliced_grid is not None and slice_ is None: - self.grid = sliced_grid - elif slice_ is not None and sliced_grid is None: - self.grid = self.parent.slicer[slice_] - elif sliced_grid is not None and slice_ is not None: - raise RuntimeError( - "PlutoDataSlice: Only one of sliced_grid or slice_ can be set" - ) - else: - raise RuntimeError( - "PlutoDataSlice: Either sliced_grid or slice_ must be set" - ) + self.slicer = None def __getitem__(self, var: str) -> np.memmap: return self.parent[var][self.grid.slice] diff --git a/plutoplot/scripts.py b/plutoplot/scripts.py index 61196b5..2619715 100644 --- a/plutoplot/scripts.py +++ b/plutoplot/scripts.py @@ -2,7 +2,7 @@ import argparse -def format_ini(): +def format_ini() -> None: """Entrypoint to format `pluto.ini` file""" from .metadata import Pluto_ini diff --git a/plutoplot/simulation.py b/plutoplot/simulation.py index 4b94971..6595bb2 100644 --- a/plutoplot/simulation.py +++ b/plutoplot/simulation.py @@ -36,6 +36,22 @@ def __init__( coordinates: str = None, indexing: str = "ijk", ): + """Create Simulation object from PLUTO output directory + + Args: + path (Path or str, optional): Path to simulation directory / data directory + format (str, optional): PLUTO output format to load. + Currently supported: 'dbl', 'flt', 'vtk', 'dbl.h5', 'flt.h5'. + By default uses the first {format}.out file found. + coordinates (str, optional): name of coordinates system of simulation. + Will be read from gridfile by default + Supported: (') + indexing (str, optional): Array index convention. Supports ("ijk", "kji"). + + Raises: + FileNotFoundError: if no metadata or grid files are found. + NotImplementedError: if unsupported format is requested + """ self.parent = None self.path = Path(path) @@ -85,7 +101,9 @@ def __init__( self.grid = Grid(self.data_path / "grid.out", coordinates, indexing=indexing) # slicer - self.slicer = Slicer(lambda slice_: SimulationSlice(self, slice_)) + self.slicer = Slicer( + lambda slice_: SimulationSlice(self, self.grid.slicer[slice_]) + ) # PlutoData cache self._data = {} @@ -290,7 +308,7 @@ def handler(i): handler, i=widgets.IntSlider(min=0, max=len(self) - 1, value=self._index(n)), ) - plot.children[0].description = "Simulation frame" + plot.children[0].description = "Step" plot.children[0].layout.width = "40%" display(plot) @@ -308,17 +326,12 @@ def clear(self) -> None: def __str__(self) -> str: return ( - f"PLUTO {type(self).__name__} at '{self.path}'\n" - f"Data directory at '$SIM_DIR/{self.data_path.relative_to(self.path)}'\n" - f"{self.grid.coordinates.capitalize()} grid with dimensions {self.dims}\n" - f"Domain: x1: {self.x1l[0]:.2e} .. {self.x1r[-1]:.2e} (Lx1 = {self.Lx1:.2e})\n" - f" x2: {self.x2l[0]:.2e} .. {self.x2r[-1]:.2e} (Lx2 = {self.Lx2:.2e})\n" - f" x2: {self.x3l[0]:.2e} .. {self.x3r[-1]:.2e} (Lx3 = {self.Lx3:.2e})\n" - f"Available variables: {' '.join(self.vars)}\n" - "Data files:\n" - f" Format {self.format}: {len(self)} files, " - f"last time {self.t[-1]}, data timestep {self.dt.mean():.2e}\n" - ) + f"PLUTO {type(self).__name__}: path: '{self.path}', " + f"data directory '$sim_path/{self.data_path.relative_to(self.path)}'\n" + f"Data vars: {', '.join(self.metadata.vars)}\n" + f"Data files: Format `{self.format}`: {len(self)} files," + f" last time {self.t[-1]}, data timestep {self.dt.mean():.2e} \n" + ) + str(self.grid) def __repr__(self) -> str: return ( @@ -404,14 +417,14 @@ def __repr__(self) -> str: class SimulationSlice(Simulation): - def __init__(self, parent, slice_): + def __init__(self, parent, sliced_grid): self.parent = parent self.path = self.parent.path self.data_path = self.parent.data_path self.format = self.parent.format self.metadata = self.parent.metadata - self.grid = self.parent.grid.slicer[slice_] + self.grid = sliced_grid self.slicer = None diff --git a/poetry.lock b/poetry.lock new file mode 100644 index 0000000..eadb358 --- /dev/null +++ b/poetry.lock @@ -0,0 +1,2010 @@ +[[package]] +name = "appnope" +version = "0.1.2" +description = "Disable App Nap on macOS >= 10.9" +category = "main" +optional = true +python-versions = "*" + +[[package]] +name = "argon2-cffi" +version = "21.3.0" +description = "The secure Argon2 password hashing algorithm." +category = "main" +optional = true +python-versions = ">=3.6" + +[package.dependencies] +argon2-cffi-bindings = "*" +typing-extensions = {version = "*", markers = "python_version < \"3.8\""} + +[package.extras] +dev = ["pre-commit", "cogapp", "tomli", "coverage[toml] (>=5.0.2)", "hypothesis", "pytest", "sphinx", 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+[tool.poetry.dependencies] +python = ">=3.7,<3.11" +numpy = "^1.19" +matplotlib = "^3.3" +h5py = { version = "^3.0", optional = true } +ipywidgets = { version = "^7.0", optional = true } + +[tool.poetry.extras] +hdf5 = ["h5py"] +interactive = ["ipywidgets"] + +[tool.poetry.dev-dependencies] +pytest = "^7.1.1" +tox = "^3.24.5" +tox-gh-actions = "^2.9.1" +mypy = "^0.942" +pre-commit = "^2.17.0" + +[build-system] +requires = ["poetry-core"] +build-backend = "poetry.core.masonry.api" diff --git a/setup.cfg b/setup.cfg deleted file mode 100644 index 9b2692c..0000000 --- a/setup.cfg +++ /dev/null @@ -1,26 +0,0 @@ -[metadata] -name = plutoplot -author = Simeon Doetsch -author_email = science@simske.com -url = https://gitlab.com/simske/plutoplot - -[options] -packages = plutoplot -install_requires = - numpy - matplotlib - -[options.entry_points] -console_scripts = - pluto-format-ini = plutoplot.scripts:format_ini - pluto-info = plutoplot.info:main - -[options.extras_require] -interactive = ipywidgets -hdf5 = h5py - -[versioneer] -VCS = git -style = pep440 -versionfile_source = plutoplot/_version.py -tag_prefix = v diff --git a/setup.py b/setup.py deleted file mode 100644 index 8c8e1bb..0000000 --- a/setup.py +++ /dev/null @@ -1,6 +0,0 @@ -"Install plutoplot package using setup.cfg" -import setuptools - -import versioneer - -setuptools.setup(version=versioneer.get_version(), cmdclass=versioneer.get_cmdclass()) diff --git a/test/test_grid.py b/test/test_grid.py new file mode 100644 index 0000000..3ca3934 --- /dev/null +++ b/test/test_grid.py @@ -0,0 +1,58 @@ +import random + +import numpy as np +import pytest + +from plutoplot.grid import Grid, normalize_slice + +random.seed(23951305348253) + + +class TestNormaliceSlice: + @pytest.fixture + def dims(self): + return tuple(random.randint(10, 1000) for _ in range(3)) + + def test_empty(self, dims): + assert normalize_slice(np.s_[:, :, :], dims) == tuple( + slice(0, dim, 1) for dim in dims + ) + + def test_inbounds(self, dims): + starts = tuple(random.randint(0, dim) for dim in dims) + stops = tuple(random.randint(start, dim) for start, dim in zip(starts, dims)) + assert normalize_slice( + np.s_[starts[0] : stops[0], starts[1] : stops[1], starts[2] : stops[2]], + dims, + ) == tuple(slice(start, stop, 1) for start, stop in zip(starts, stops)) + + def test_outofbounds(self, dims): + with pytest.raises(IndexError): + normalize_slice(np.s_[0 : dims[0] + 1, :, :], dims) + with pytest.raises(IndexError): + normalize_slice(np.s_[dims[0] :, :, :], dims) + + def test_negative(self, dims): + starts = tuple(-random.randint(0, dim - 1) for dim in dims) + stops = tuple(random.randint(start, 0) for start in starts) + + assert normalize_slice( + np.s_[starts[0] : stops[0], starts[1] : stops[1], starts[2] : stops[2]], + dims, + ) == tuple( + slice(dim + start, dim + stop, 1) + for dim, start, stop in zip(dims, starts, stops) + ) + + def test_1high_slice(self, dims): + starts = tuple(random.randint(0, dim) for dim in dims) + stops = ( + random.randint(starts[0], dims[0]), + starts[1] + 1, + random.randint(starts[2], dims[2]), + ) + + assert normalize_slice( + np.s_[starts[0] : stops[0], starts[1], starts[2] : stops[2]], + dims, + ) == tuple(slice(start, stop, 1) for start, stop in zip(starts, stops)) diff --git a/test/test_io.py b/test/test_io.py deleted file mode 100644 index 6cfdecf..0000000 --- a/test/test_io.py +++ /dev/null @@ -1,33 +0,0 @@ -import os -import unittest - -import numpy as np -from generate_testdata import generate_gridfile - -from plutoplot.grid import Grid - - -class TestGrid(unittest.TestCase): - def setUp(self): - self.file = "gridtest.out" - self.dims = (10, 11, 12) - generate_gridfile(self.file, self.dims) - self.grid = Grid(self.file) - - def tearDown(self): - os.remove(self.file) - - def testDimensions(self): - self.assertEqual(self.dims, self.grid.dims) - self.assertEqual(self.dims, self.grid.data_shape) - - def testData(self): - for i, res in enumerate(self.dims, start=1): - x = getattr(self.grid, f"x{i}") - dx = getattr(self.grid, f"dx{i}") - np.testing.assert_array_almost_equal_nulp(x, np.arange(0.5, res, 1)) - np.testing.assert_array_almost_equal_nulp(dx, np.ones(res)) - - -if __name__ == "__main__": - unittest.main() diff --git a/tox.ini b/tox.ini new file mode 100644 index 0000000..71297f9 --- /dev/null +++ b/tox.ini @@ -0,0 +1,15 @@ +[tox] +envlist = py37,py38,py39,py310 +isolated_build = true + +[gh-actions] +python = + 3.7: py37 + 3.8: py38 + 3.9: py39 + 3.10: py310 + +[testenv] +deps = + pytest +commands = pytest diff --git a/versioneer.py b/versioneer.py deleted file mode 100644 index 2b54540..0000000 --- a/versioneer.py +++ /dev/null @@ -1,1885 +0,0 @@ -# Version: 0.18 - -"""The Versioneer - like a rocketeer, but for versions. - -The Versioneer -============== - -* like a rocketeer, but for versions! -* https://github.com/warner/python-versioneer -* Brian Warner -* License: Public Domain -* Compatible With: python2.6, 2.7, 3.2, 3.3, 3.4, 3.5, 3.6, and pypy -* [![Latest Version] -(https://pypip.in/version/versioneer/badge.svg?style=flat) -](https://pypi.python.org/pypi/versioneer/) -* [![Build Status] -(https://travis-ci.org/warner/python-versioneer.png?branch=master) -](https://travis-ci.org/warner/python-versioneer) - -This is a tool for managing a recorded version number in distutils-based -python projects. The goal is to remove the tedious and error-prone "update -the embedded version string" step from your release process. Making a new -release should be as easy as recording a new tag in your version-control -system, and maybe making new tarballs. - - -## Quick Install - -* `pip install versioneer` to somewhere to your $PATH -* add a `[versioneer]` section to your setup.cfg (see below) -* run `versioneer install` in your source tree, commit the results - -## Version Identifiers - -Source trees come from a variety of places: - -* a version-control system checkout (mostly used by developers) -* a nightly tarball, produced by build automation -* a snapshot tarball, produced by a web-based VCS browser, like github's - "tarball from tag" feature -* a release tarball, produced by "setup.py sdist", distributed through PyPI - -Within each source tree, the version identifier (either a string or a number, -this tool is format-agnostic) can come from a variety of places: - -* ask the VCS tool itself, e.g. "git describe" (for checkouts), which knows - about recent "tags" and an absolute revision-id -* the name of the directory into which the tarball was unpacked -* an expanded VCS keyword ($Id$, etc) -* a `_version.py` created by some earlier build step - -For released software, the version identifier is closely related to a VCS -tag. Some projects use tag names that include more than just the version -string (e.g. "myproject-1.2" instead of just "1.2"), in which case the tool -needs to strip the tag prefix to extract the version identifier. For -unreleased software (between tags), the version identifier should provide -enough information to help developers recreate the same tree, while also -giving them an idea of roughly how old the tree is (after version 1.2, before -version 1.3). Many VCS systems can report a description that captures this, -for example `git describe --tags --dirty --always` reports things like -"0.7-1-g574ab98-dirty" to indicate that the checkout is one revision past the -0.7 tag, has a unique revision id of "574ab98", and is "dirty" (it has -uncommitted changes. - -The version identifier is used for multiple purposes: - -* to allow the module to self-identify its version: `myproject.__version__` -* to choose a name and prefix for a 'setup.py sdist' tarball - -## Theory of Operation - -Versioneer works by adding a special `_version.py` file into your source -tree, where your `__init__.py` can import it. This `_version.py` knows how to -dynamically ask the VCS tool for version information at import time. - -`_version.py` also contains `$Revision$` markers, and the installation -process marks `_version.py` to have this marker rewritten with a tag name -during the `git archive` command. As a result, generated tarballs will -contain enough information to get the proper version. - -To allow `setup.py` to compute a version too, a `versioneer.py` is added to -the top level of your source tree, next to `setup.py` and the `setup.cfg` -that configures it. This overrides several distutils/setuptools commands to -compute the version when invoked, and changes `setup.py build` and `setup.py -sdist` to replace `_version.py` with a small static file that contains just -the generated version data. - -## Installation - -See [INSTALL.md](./INSTALL.md) for detailed installation instructions. - -## Version-String Flavors - -Code which uses Versioneer can learn about its version string at runtime by -importing `_version` from your main `__init__.py` file and running the -`get_versions()` function. From the "outside" (e.g. in `setup.py`), you can -import the top-level `versioneer.py` and run `get_versions()`. - -Both functions return a dictionary with different flavors of version -information: - -* `['version']`: A condensed version string, rendered using the selected - style. This is the most commonly used value for the project's version - string. The default "pep440" style yields strings like `0.11`, - `0.11+2.g1076c97`, or `0.11+2.g1076c97.dirty`. See the "Styles" section - below for alternative styles. - -* `['full-revisionid']`: detailed revision identifier. For Git, this is the - full SHA1 commit id, e.g. "1076c978a8d3cfc70f408fe5974aa6c092c949ac". - -* `['date']`: Date and time of the latest `HEAD` commit. For Git, it is the - commit date in ISO 8601 format. This will be None if the date is not - available. - -* `['dirty']`: a boolean, True if the tree has uncommitted changes. Note that - this is only accurate if run in a VCS checkout, otherwise it is likely to - be False or None - -* `['error']`: if the version string could not be computed, this will be set - to a string describing the problem, otherwise it will be None. It may be - useful to throw an exception in setup.py if this is set, to avoid e.g. - creating tarballs with a version string of "unknown". - -Some variants are more useful than others. Including `full-revisionid` in a -bug report should allow developers to reconstruct the exact code being tested -(or indicate the presence of local changes that should be shared with the -developers). `version` is suitable for display in an "about" box or a CLI -`--version` output: it can be easily compared against release notes and lists -of bugs fixed in various releases. - -The installer adds the following text to your `__init__.py` to place a basic -version in `YOURPROJECT.__version__`: - - from ._version import get_versions - __version__ = get_versions()['version'] - del get_versions - -## Styles - -The setup.cfg `style=` configuration controls how the VCS information is -rendered into a version string. - -The default style, "pep440", produces a PEP440-compliant string, equal to the -un-prefixed tag name for actual releases, and containing an additional "local -version" section with more detail for in-between builds. For Git, this is -TAG[+DISTANCE.gHEX[.dirty]] , using information from `git describe --tags ---dirty --always`. For example "0.11+2.g1076c97.dirty" indicates that the -tree is like the "1076c97" commit but has uncommitted changes (".dirty"), and -that this commit is two revisions ("+2") beyond the "0.11" tag. For released -software (exactly equal to a known tag), the identifier will only contain the -stripped tag, e.g. "0.11". - -Other styles are available. See [details.md](details.md) in the Versioneer -source tree for descriptions. - -## Debugging - -Versioneer tries to avoid fatal errors: if something goes wrong, it will tend -to return a version of "0+unknown". To investigate the problem, run `setup.py -version`, which will run the version-lookup code in a verbose mode, and will -display the full contents of `get_versions()` (including the `error` string, -which may help identify what went wrong). - -## Known Limitations - -Some situations are known to cause problems for Versioneer. This details the -most significant ones. More can be found on Github -[issues page](https://github.com/warner/python-versioneer/issues). - -### Subprojects - -Versioneer has limited support for source trees in which `setup.py` is not in -the root directory (e.g. `setup.py` and `.git/` are *not* siblings). The are -two common reasons why `setup.py` might not be in the root: - -* Source trees which contain multiple subprojects, such as - [Buildbot](https://github.com/buildbot/buildbot), which contains both - "master" and "slave" subprojects, each with their own `setup.py`, - `setup.cfg`, and `tox.ini`. Projects like these produce multiple PyPI - distributions (and upload multiple independently-installable tarballs). -* Source trees whose main purpose is to contain a C library, but which also - provide bindings to Python (and perhaps other langauges) in subdirectories. - -Versioneer will look for `.git` in parent directories, and most operations -should get the right version string. However `pip` and `setuptools` have bugs -and implementation details which frequently cause `pip install .` from a -subproject directory to fail to find a correct version string (so it usually -defaults to `0+unknown`). - -`pip install --editable .` should work correctly. `setup.py install` might -work too. - -Pip-8.1.1 is known to have this problem, but hopefully it will get fixed in -some later version. - -[Bug #38](https://github.com/warner/python-versioneer/issues/38) is tracking -this issue. The discussion in -[PR #61](https://github.com/warner/python-versioneer/pull/61) describes the -issue from the Versioneer side in more detail. -[pip PR#3176](https://github.com/pypa/pip/pull/3176) and -[pip PR#3615](https://github.com/pypa/pip/pull/3615) contain work to improve -pip to let Versioneer work correctly. - -Versioneer-0.16 and earlier only looked for a `.git` directory next to the -`setup.cfg`, so subprojects were completely unsupported with those releases. - -### Editable installs with setuptools <= 18.5 - -`setup.py develop` and `pip install --editable .` allow you to install a -project into a virtualenv once, then continue editing the source code (and -test) without re-installing after every change. - -"Entry-point scripts" (`setup(entry_points={"console_scripts": ..})`) are a -convenient way to specify executable scripts that should be installed along -with the python package. - -These both work as expected when using modern setuptools. When using -setuptools-18.5 or earlier, however, certain operations will cause -`pkg_resources.DistributionNotFound` errors when running the entrypoint -script, which must be resolved by re-installing the package. This happens -when the install happens with one version, then the egg_info data is -regenerated while a different version is checked out. Many setup.py commands -cause egg_info to be rebuilt (including `sdist`, `wheel`, and installing into -a different virtualenv), so this can be surprising. - -[Bug #83](https://github.com/warner/python-versioneer/issues/83) describes -this one, but upgrading to a newer version of setuptools should probably -resolve it. - -### Unicode version strings - -While Versioneer works (and is continually tested) with both Python 2 and -Python 3, it is not entirely consistent with bytes-vs-unicode distinctions. -Newer releases probably generate unicode version strings on py2. It's not -clear that this is wrong, but it may be surprising for applications when then -write these strings to a network connection or include them in bytes-oriented -APIs like cryptographic checksums. - -[Bug #71](https://github.com/warner/python-versioneer/issues/71) investigates -this question. - - -## Updating Versioneer - -To upgrade your project to a new release of Versioneer, do the following: - -* install the new Versioneer (`pip install -U versioneer` or equivalent) -* edit `setup.cfg`, if necessary, to include any new configuration settings - indicated by the release notes. See [UPGRADING](./UPGRADING.md) for details. -* re-run `versioneer install` in your source tree, to replace - `SRC/_version.py` -* commit any changed files - -## Future Directions - -This tool is designed to make it easily extended to other version-control -systems: all VCS-specific components are in separate directories like -src/git/ . The top-level `versioneer.py` script is assembled from these -components by running make-versioneer.py . In the future, make-versioneer.py -will take a VCS name as an argument, and will construct a version of -`versioneer.py` that is specific to the given VCS. It might also take the -configuration arguments that are currently provided manually during -installation by editing setup.py . Alternatively, it might go the other -direction and include code from all supported VCS systems, reducing the -number of intermediate scripts. - - -## License - -To make Versioneer easier to embed, all its code is dedicated to the public -domain. The `_version.py` that it creates is also in the public domain. -Specifically, both are released under the Creative Commons "Public Domain -Dedication" license (CC0-1.0), as described in -https://creativecommons.org/publicdomain/zero/1.0/ . - -""" - -from __future__ import print_function - -try: - import configparser -except ImportError: - import ConfigParser as configparser -import errno -import json -import os -import re -import subprocess -import sys - - -class VersioneerConfig: - """Container for Versioneer configuration parameters.""" - - -def get_root(): - """Get the project root directory. - - We require that all commands are run from the project root, i.e. the - directory that contains setup.py, setup.cfg, and versioneer.py . - """ - root = os.path.realpath(os.path.abspath(os.getcwd())) - setup_py = os.path.join(root, "setup.py") - versioneer_py = os.path.join(root, "versioneer.py") - if not (os.path.exists(setup_py) or os.path.exists(versioneer_py)): - # allow 'python path/to/setup.py COMMAND' - root = os.path.dirname(os.path.realpath(os.path.abspath(sys.argv[0]))) - setup_py = os.path.join(root, "setup.py") - versioneer_py = os.path.join(root, "versioneer.py") - if not (os.path.exists(setup_py) or os.path.exists(versioneer_py)): - err = ( - "Versioneer was unable to run the project root directory. " - "Versioneer requires setup.py to be executed from " - "its immediate directory (like 'python setup.py COMMAND'), " - "or in a way that lets it use sys.argv[0] to find the root " - "(like 'python path/to/setup.py COMMAND')." - ) - raise VersioneerBadRootError(err) - try: - # Certain runtime workflows (setup.py install/develop in a setuptools - # tree) execute all dependencies in a single python process, so - # "versioneer" may be imported multiple times, and python's shared - # module-import table will cache the first one. So we can't use - # os.path.dirname(__file__), as that will find whichever - # versioneer.py was first imported, even in later projects. - me = os.path.realpath(os.path.abspath(__file__)) - me_dir = os.path.normcase(os.path.splitext(me)[0]) - vsr_dir = os.path.normcase(os.path.splitext(versioneer_py)[0]) - if me_dir != vsr_dir: - print( - "Warning: build in %s is using versioneer.py from %s" - % (os.path.dirname(me), versioneer_py) - ) - except NameError: - pass - return root - - -def get_config_from_root(root): - """Read the project setup.cfg file to determine Versioneer config.""" - # This might raise EnvironmentError (if setup.cfg is missing), or - # configparser.NoSectionError (if it lacks a [versioneer] section), or - # configparser.NoOptionError (if it lacks "VCS="). See the docstring at - # the top of versioneer.py for instructions on writing your setup.cfg . - setup_cfg = os.path.join(root, "setup.cfg") - parser = configparser.SafeConfigParser() - with open(setup_cfg, "r") as f: - parser.readfp(f) - VCS = parser.get("versioneer", "VCS") # mandatory - - def get(parser, name): - if parser.has_option("versioneer", name): - return parser.get("versioneer", name) - return None - - cfg = VersioneerConfig() - cfg.VCS = VCS - cfg.style = get(parser, "style") or "" - cfg.versionfile_source = get(parser, "versionfile_source") - cfg.versionfile_build = get(parser, "versionfile_build") - cfg.tag_prefix = get(parser, "tag_prefix") - if cfg.tag_prefix in ("''", '""'): - cfg.tag_prefix = "" - cfg.parentdir_prefix = get(parser, "parentdir_prefix") - cfg.verbose = get(parser, "verbose") - return cfg - - -class NotThisMethod(Exception): - """Exception raised if a method is not valid for the current scenario.""" - - -# these dictionaries contain VCS-specific tools -LONG_VERSION_PY = {} -HANDLERS = {} - - -def register_vcs_handler(vcs, method): # decorator - """Decorator to mark a method as the handler for a particular VCS.""" - - def decorate(f): - """Store f in HANDLERS[vcs][method].""" - if vcs not in HANDLERS: - HANDLERS[vcs] = {} - HANDLERS[vcs][method] = f - return f - - return decorate - - -def run_command(commands, args, cwd=None, verbose=False, hide_stderr=False, env=None): - """Call the given command(s).""" - assert isinstance(commands, list) - p = None - for c in commands: - try: - dispcmd = str([c] + args) - # remember shell=False, so use git.cmd on windows, not just git - p = subprocess.Popen( - [c] + args, - cwd=cwd, - env=env, - stdout=subprocess.PIPE, - stderr=(subprocess.PIPE if hide_stderr else None), - ) - break - except EnvironmentError: - e = sys.exc_info()[1] - if e.errno == errno.ENOENT: - continue - if verbose: - print("unable to run %s" % dispcmd) - print(e) - return None, None - else: - if verbose: - print("unable to find command, tried %s" % (commands,)) - return None, None - stdout = p.communicate()[0].strip() - if sys.version_info[0] >= 3: - stdout = stdout.decode() - if p.returncode != 0: - if verbose: - print("unable to run %s (error)" % dispcmd) - print("stdout was %s" % stdout) - return None, p.returncode - return stdout, p.returncode - - -LONG_VERSION_PY[ - "git" -] = ''' -# This file helps to compute a version number in source trees obtained from -# git-archive tarball (such as those provided by githubs download-from-tag -# feature). Distribution tarballs (built by setup.py sdist) and build -# directories (produced by setup.py build) will contain a much shorter file -# that just contains the computed version number. - -# This file is released into the public domain. Generated by -# versioneer-0.18 (https://github.com/warner/python-versioneer) - -"""Git implementation of _version.py.""" - -import errno -import os -import re -import subprocess -import sys - - -def get_keywords(): - """Get the keywords needed to look up the version information.""" - # these strings will be replaced by git during git-archive. - # setup.py/versioneer.py will grep for the variable names, so they must - # each be defined on a line of their own. _version.py will just call - # get_keywords(). - git_refnames = "%(DOLLAR)sFormat:%%d%(DOLLAR)s" - git_full = "%(DOLLAR)sFormat:%%H%(DOLLAR)s" - git_date = "%(DOLLAR)sFormat:%%ci%(DOLLAR)s" - keywords = {"refnames": git_refnames, "full": git_full, "date": git_date} - return keywords - - -class VersioneerConfig: - """Container for Versioneer configuration parameters.""" - - -def get_config(): - """Create, populate and return the VersioneerConfig() object.""" - # these strings are filled in when 'setup.py versioneer' creates - # _version.py - cfg = VersioneerConfig() - cfg.VCS = "git" - cfg.style = "%(STYLE)s" - cfg.tag_prefix = "%(TAG_PREFIX)s" - cfg.parentdir_prefix = "%(PARENTDIR_PREFIX)s" - cfg.versionfile_source = "%(VERSIONFILE_SOURCE)s" - cfg.verbose = False - return cfg - - -class NotThisMethod(Exception): - """Exception raised if a method is not valid for the current scenario.""" - - -LONG_VERSION_PY = {} -HANDLERS = {} - - -def register_vcs_handler(vcs, method): # decorator - """Decorator to mark a method as the handler for a particular VCS.""" - def decorate(f): - """Store f in HANDLERS[vcs][method].""" - if vcs not in HANDLERS: - HANDLERS[vcs] = {} - HANDLERS[vcs][method] = f - return f - return decorate - - -def run_command(commands, args, cwd=None, verbose=False, hide_stderr=False, - env=None): - """Call the given command(s).""" - assert isinstance(commands, list) - p = None - for c in commands: - try: - dispcmd = str([c] + args) - # remember shell=False, so use git.cmd on windows, not just git - p = subprocess.Popen([c] + args, cwd=cwd, env=env, - stdout=subprocess.PIPE, - stderr=(subprocess.PIPE if hide_stderr - else None)) - break - except EnvironmentError: - e = sys.exc_info()[1] - if e.errno == errno.ENOENT: - continue - if verbose: - print("unable to run %%s" %% dispcmd) - print(e) - return None, None - else: - if verbose: - print("unable to find command, tried %%s" %% (commands,)) - return None, None - stdout = p.communicate()[0].strip() - if sys.version_info[0] >= 3: - stdout = stdout.decode() - if p.returncode != 0: - if verbose: - print("unable to run %%s (error)" %% dispcmd) - print("stdout was %%s" %% stdout) - return None, p.returncode - return stdout, p.returncode - - -def versions_from_parentdir(parentdir_prefix, root, verbose): - """Try to determine the version from the parent directory name. - - Source tarballs conventionally unpack into a directory that includes both - the project name and a version string. We will also support searching up - two directory levels for an appropriately named parent directory - """ - rootdirs = [] - - for i in range(3): - dirname = os.path.basename(root) - if dirname.startswith(parentdir_prefix): - return {"version": dirname[len(parentdir_prefix):], - "full-revisionid": None, - "dirty": False, "error": None, "date": None} - else: - rootdirs.append(root) - root = os.path.dirname(root) # up a level - - if verbose: - print("Tried directories %%s but none started with prefix %%s" %% - (str(rootdirs), parentdir_prefix)) - raise NotThisMethod("rootdir doesn't start with parentdir_prefix") - - -@register_vcs_handler("git", "get_keywords") -def git_get_keywords(versionfile_abs): - """Extract version information from the given file.""" - # the code embedded in _version.py can just fetch the value of these - # keywords. When used from setup.py, we don't want to import _version.py, - # so we do it with a regexp instead. This function is not used from - # _version.py. - keywords = {} - try: - f = open(versionfile_abs, "r") - for line in f.readlines(): - if line.strip().startswith("git_refnames ="): - mo = re.search(r'=\s*"(.*)"', line) - if mo: - keywords["refnames"] = mo.group(1) - if line.strip().startswith("git_full ="): - mo = re.search(r'=\s*"(.*)"', line) - if mo: - keywords["full"] = mo.group(1) - if line.strip().startswith("git_date ="): - mo = re.search(r'=\s*"(.*)"', line) - if mo: - keywords["date"] = mo.group(1) - f.close() - except EnvironmentError: - pass - return keywords - - -@register_vcs_handler("git", "keywords") -def git_versions_from_keywords(keywords, tag_prefix, verbose): - """Get version information from git keywords.""" - if not keywords: - raise NotThisMethod("no keywords at all, weird") - date = keywords.get("date") - if date is not None: - # git-2.2.0 added "%%cI", which expands to an ISO-8601 -compliant - # datestamp. However we prefer "%%ci" (which expands to an "ISO-8601 - # -like" string, which we must then edit to make compliant), because - # it's been around since git-1.5.3, and it's too difficult to - # discover which version we're using, or to work around using an - # older one. - date = date.strip().replace(" ", "T", 1).replace(" ", "", 1) - refnames = keywords["refnames"].strip() - if refnames.startswith("$Format"): - if verbose: - print("keywords are unexpanded, not using") - raise NotThisMethod("unexpanded keywords, not a git-archive tarball") - refs = set([r.strip() for r in refnames.strip("()").split(",")]) - # starting in git-1.8.3, tags are listed as "tag: foo-1.0" instead of - # just "foo-1.0". If we see a "tag: " prefix, prefer those. - TAG = "tag: " - tags = set([r[len(TAG):] for r in refs if r.startswith(TAG)]) - if not tags: - # Either we're using git < 1.8.3, or there really are no tags. We use - # a heuristic: assume all version tags have a digit. The old git %%d - # expansion behaves like git log --decorate=short and strips out the - # refs/heads/ and refs/tags/ prefixes that would let us distinguish - # between branches and tags. By ignoring refnames without digits, we - # filter out many common branch names like "release" and - # "stabilization", as well as "HEAD" and "master". - tags = set([r for r in refs if re.search(r'\d', r)]) - if verbose: - print("discarding '%%s', no digits" %% ",".join(refs - tags)) - if verbose: - print("likely tags: %%s" %% ",".join(sorted(tags))) - for ref in sorted(tags): - # sorting will prefer e.g. "2.0" over "2.0rc1" - if ref.startswith(tag_prefix): - r = ref[len(tag_prefix):] - if verbose: - print("picking %%s" %% r) - return {"version": r, - "full-revisionid": keywords["full"].strip(), - "dirty": False, "error": None, - "date": date} - # no suitable tags, so version is "0+unknown", but full hex is still there - if verbose: - print("no suitable tags, using unknown + full revision id") - return {"version": "0+unknown", - "full-revisionid": keywords["full"].strip(), - "dirty": False, "error": "no suitable tags", "date": None} - - -@register_vcs_handler("git", "pieces_from_vcs") -def git_pieces_from_vcs(tag_prefix, root, verbose, run_command=run_command): - """Get version from 'git describe' in the root of the source tree. - - This only gets called if the git-archive 'subst' keywords were *not* - expanded, and _version.py hasn't already been rewritten with a short - version string, meaning we're inside a checked out source tree. - """ - GITS = ["git"] - if sys.platform == "win32": - GITS = ["git.cmd", "git.exe"] - - out, rc = run_command(GITS, ["rev-parse", "--git-dir"], cwd=root, - hide_stderr=True) - if rc != 0: - if verbose: - print("Directory %%s not under git control" %% root) - raise NotThisMethod("'git rev-parse --git-dir' returned error") - - # if there is a tag matching tag_prefix, this yields TAG-NUM-gHEX[-dirty] - # if there isn't one, this yields HEX[-dirty] (no NUM) - describe_out, rc = run_command(GITS, ["describe", "--tags", "--dirty", - "--always", "--long", - "--match", "%%s*" %% tag_prefix], - cwd=root) - # --long was added in git-1.5.5 - if describe_out is None: - raise NotThisMethod("'git describe' failed") - describe_out = describe_out.strip() - full_out, rc = run_command(GITS, ["rev-parse", "HEAD"], cwd=root) - if full_out is None: - raise NotThisMethod("'git rev-parse' failed") - full_out = full_out.strip() - - pieces = {} - pieces["long"] = full_out - pieces["short"] = full_out[:7] # maybe improved later - pieces["error"] = None - - # parse describe_out. It will be like TAG-NUM-gHEX[-dirty] or HEX[-dirty] - # TAG might have hyphens. - git_describe = describe_out - - # look for -dirty suffix - dirty = git_describe.endswith("-dirty") - pieces["dirty"] = dirty - if dirty: - git_describe = git_describe[:git_describe.rindex("-dirty")] - - # now we have TAG-NUM-gHEX or HEX - - if "-" in git_describe: - # TAG-NUM-gHEX - mo = re.search(r'^(.+)-(\d+)-g([0-9a-f]+)$', git_describe) - if not mo: - # unparseable. Maybe git-describe is misbehaving? - pieces["error"] = ("unable to parse git-describe output: '%%s'" - %% describe_out) - return pieces - - # tag - full_tag = mo.group(1) - if not full_tag.startswith(tag_prefix): - if verbose: - fmt = "tag '%%s' doesn't start with prefix '%%s'" - print(fmt %% (full_tag, tag_prefix)) - pieces["error"] = ("tag '%%s' doesn't start with prefix '%%s'" - %% (full_tag, tag_prefix)) - return pieces - pieces["closest-tag"] = full_tag[len(tag_prefix):] - - # distance: number of commits since tag - pieces["distance"] = int(mo.group(2)) - - # commit: short hex revision ID - pieces["short"] = mo.group(3) - - else: - # HEX: no tags - pieces["closest-tag"] = None - count_out, rc = run_command(GITS, ["rev-list", "HEAD", "--count"], - cwd=root) - pieces["distance"] = int(count_out) # total number of commits - - # commit date: see ISO-8601 comment in git_versions_from_keywords() - date = run_command(GITS, ["show", "-s", "--format=%%ci", "HEAD"], - cwd=root)[0].strip() - pieces["date"] = date.strip().replace(" ", "T", 1).replace(" ", "", 1) - - return pieces - - -def plus_or_dot(pieces): - """Return a + if we don't already have one, else return a .""" - if "+" in pieces.get("closest-tag", ""): - return "." - return "+" - - -def render_pep440(pieces): - """Build up version string, with post-release "local version identifier". - - Our goal: TAG[+DISTANCE.gHEX[.dirty]] . Note that if you - get a tagged build and then dirty it, you'll get TAG+0.gHEX.dirty - - Exceptions: - 1: no tags. git_describe was just HEX. 0+untagged.DISTANCE.gHEX[.dirty] - """ - if pieces["closest-tag"]: - rendered = pieces["closest-tag"] - if pieces["distance"] or pieces["dirty"]: - rendered += plus_or_dot(pieces) - rendered += "%%d.g%%s" %% (pieces["distance"], pieces["short"]) - if pieces["dirty"]: - rendered += ".dirty" - else: - # exception #1 - rendered = "0+untagged.%%d.g%%s" %% (pieces["distance"], - pieces["short"]) - if pieces["dirty"]: - rendered += ".dirty" - return rendered - - -def render_pep440_pre(pieces): - """TAG[.post.devDISTANCE] -- No -dirty. - - Exceptions: - 1: no tags. 0.post.devDISTANCE - """ - if pieces["closest-tag"]: - rendered = pieces["closest-tag"] - if pieces["distance"]: - rendered += ".post.dev%%d" %% pieces["distance"] - else: - # exception #1 - rendered = "0.post.dev%%d" %% pieces["distance"] - return rendered - - -def render_pep440_post(pieces): - """TAG[.postDISTANCE[.dev0]+gHEX] . - - The ".dev0" means dirty. Note that .dev0 sorts backwards - (a dirty tree will appear "older" than the corresponding clean one), - but you shouldn't be releasing software with -dirty anyways. - - Exceptions: - 1: no tags. 0.postDISTANCE[.dev0] - """ - if pieces["closest-tag"]: - rendered = pieces["closest-tag"] - if pieces["distance"] or pieces["dirty"]: - rendered += ".post%%d" %% pieces["distance"] - if pieces["dirty"]: - rendered += ".dev0" - rendered += plus_or_dot(pieces) - rendered += "g%%s" %% pieces["short"] - else: - # exception #1 - rendered = "0.post%%d" %% pieces["distance"] - if pieces["dirty"]: - rendered += ".dev0" - rendered += "+g%%s" %% pieces["short"] - return rendered - - -def render_pep440_old(pieces): - """TAG[.postDISTANCE[.dev0]] . - - The ".dev0" means dirty. - - Eexceptions: - 1: no tags. 0.postDISTANCE[.dev0] - """ - if pieces["closest-tag"]: - rendered = pieces["closest-tag"] - if pieces["distance"] or pieces["dirty"]: - rendered += ".post%%d" %% pieces["distance"] - if pieces["dirty"]: - rendered += ".dev0" - else: - # exception #1 - rendered = "0.post%%d" %% pieces["distance"] - if pieces["dirty"]: - rendered += ".dev0" - return rendered - - -def render_git_describe(pieces): - """TAG[-DISTANCE-gHEX][-dirty]. - - Like 'git describe --tags --dirty --always'. - - Exceptions: - 1: no tags. HEX[-dirty] (note: no 'g' prefix) - """ - if pieces["closest-tag"]: - rendered = pieces["closest-tag"] - if pieces["distance"]: - rendered += "-%%d-g%%s" %% (pieces["distance"], pieces["short"]) - else: - # exception #1 - rendered = pieces["short"] - if pieces["dirty"]: - rendered += "-dirty" - return rendered - - -def render_git_describe_long(pieces): - """TAG-DISTANCE-gHEX[-dirty]. - - Like 'git describe --tags --dirty --always -long'. - The distance/hash is unconditional. - - Exceptions: - 1: no tags. HEX[-dirty] (note: no 'g' prefix) - """ - if pieces["closest-tag"]: - rendered = pieces["closest-tag"] - rendered += "-%%d-g%%s" %% (pieces["distance"], pieces["short"]) - else: - # exception #1 - rendered = pieces["short"] - if pieces["dirty"]: - rendered += "-dirty" - return rendered - - -def render(pieces, style): - """Render the given version pieces into the requested style.""" - if pieces["error"]: - return {"version": "unknown", - "full-revisionid": pieces.get("long"), - "dirty": None, - "error": pieces["error"], - "date": None} - - if not style or style == "default": - style = "pep440" # the default - - if style == "pep440": - rendered = render_pep440(pieces) - elif style == "pep440-pre": - rendered = render_pep440_pre(pieces) - elif style == "pep440-post": - rendered = render_pep440_post(pieces) - elif style == "pep440-old": - rendered = render_pep440_old(pieces) - elif style == "git-describe": - rendered = render_git_describe(pieces) - elif style == "git-describe-long": - rendered = render_git_describe_long(pieces) - else: - raise ValueError("unknown style '%%s'" %% style) - - return {"version": rendered, "full-revisionid": pieces["long"], - "dirty": pieces["dirty"], "error": None, - "date": pieces.get("date")} - - -def get_versions(): - """Get version information or return default if unable to do so.""" - # I am in _version.py, which lives at ROOT/VERSIONFILE_SOURCE. If we have - # __file__, we can work backwards from there to the root. Some - # py2exe/bbfreeze/non-CPython implementations don't do __file__, in which - # case we can only use expanded keywords. - - cfg = get_config() - verbose = cfg.verbose - - try: - return git_versions_from_keywords(get_keywords(), cfg.tag_prefix, - verbose) - except NotThisMethod: - pass - - try: - root = os.path.realpath(__file__) - # versionfile_source is the relative path from the top of the source - # tree (where the .git directory might live) to this file. Invert - # this to find the root from __file__. - for i in cfg.versionfile_source.split('/'): - root = os.path.dirname(root) - except NameError: - return {"version": "0+unknown", "full-revisionid": None, - "dirty": None, - "error": "unable to find root of source tree", - "date": None} - - try: - pieces = git_pieces_from_vcs(cfg.tag_prefix, root, verbose) - return render(pieces, cfg.style) - except NotThisMethod: - pass - - try: - if cfg.parentdir_prefix: - return versions_from_parentdir(cfg.parentdir_prefix, root, verbose) - except NotThisMethod: - pass - - return {"version": "0+unknown", "full-revisionid": None, - "dirty": None, - "error": "unable to compute version", "date": None} -''' - - -@register_vcs_handler("git", "get_keywords") -def git_get_keywords(versionfile_abs): - """Extract version information from the given file.""" - # the code embedded in _version.py can just fetch the value of these - # keywords. When used from setup.py, we don't want to import _version.py, - # so we do it with a regexp instead. This function is not used from - # _version.py. - keywords = {} - try: - f = open(versionfile_abs, "r") - for line in f.readlines(): - if line.strip().startswith("git_refnames ="): - mo = re.search(r'=\s*"(.*)"', line) - if mo: - keywords["refnames"] = mo.group(1) - if line.strip().startswith("git_full ="): - mo = re.search(r'=\s*"(.*)"', line) - if mo: - keywords["full"] = mo.group(1) - if line.strip().startswith("git_date ="): - mo = re.search(r'=\s*"(.*)"', line) - if mo: - keywords["date"] = mo.group(1) - f.close() - except EnvironmentError: - pass - return keywords - - -@register_vcs_handler("git", "keywords") -def git_versions_from_keywords(keywords, tag_prefix, verbose): - """Get version information from git keywords.""" - if not keywords: - raise NotThisMethod("no keywords at all, weird") - date = keywords.get("date") - if date is not None: - # git-2.2.0 added "%cI", which expands to an ISO-8601 -compliant - # datestamp. However we prefer "%ci" (which expands to an "ISO-8601 - # -like" string, which we must then edit to make compliant), because - # it's been around since git-1.5.3, and it's too difficult to - # discover which version we're using, or to work around using an - # older one. - date = date.strip().replace(" ", "T", 1).replace(" ", "", 1) - refnames = keywords["refnames"].strip() - if refnames.startswith("$Format"): - if verbose: - print("keywords are unexpanded, not using") - raise NotThisMethod("unexpanded keywords, not a git-archive tarball") - refs = set([r.strip() for r in refnames.strip("()").split(",")]) - # starting in git-1.8.3, tags are listed as "tag: foo-1.0" instead of - # just "foo-1.0". If we see a "tag: " prefix, prefer those. - TAG = "tag: " - tags = set([r[len(TAG) :] for r in refs if r.startswith(TAG)]) - if not tags: - # Either we're using git < 1.8.3, or there really are no tags. We use - # a heuristic: assume all version tags have a digit. The old git %d - # expansion behaves like git log --decorate=short and strips out the - # refs/heads/ and refs/tags/ prefixes that would let us distinguish - # between branches and tags. By ignoring refnames without digits, we - # filter out many common branch names like "release" and - # "stabilization", as well as "HEAD" and "master". - tags = set([r for r in refs if re.search(r"\d", r)]) - if verbose: - print("discarding '%s', no digits" % ",".join(refs - tags)) - if verbose: - print("likely tags: %s" % ",".join(sorted(tags))) - for ref in sorted(tags): - # sorting will prefer e.g. "2.0" over "2.0rc1" - if ref.startswith(tag_prefix): - r = ref[len(tag_prefix) :] - if verbose: - print("picking %s" % r) - return { - "version": r, - "full-revisionid": keywords["full"].strip(), - "dirty": False, - "error": None, - "date": date, - } - # no suitable tags, so version is "0+unknown", but full hex is still there - if verbose: - print("no suitable tags, using unknown + full revision id") - return { - "version": "0+unknown", - "full-revisionid": keywords["full"].strip(), - "dirty": False, - "error": "no suitable tags", - "date": None, - } - - -@register_vcs_handler("git", "pieces_from_vcs") -def git_pieces_from_vcs(tag_prefix, root, verbose, run_command=run_command): - """Get version from 'git describe' in the root of the source tree. - - This only gets called if the git-archive 'subst' keywords were *not* - expanded, and _version.py hasn't already been rewritten with a short - version string, meaning we're inside a checked out source tree. - """ - GITS = ["git"] - if sys.platform == "win32": - GITS = ["git.cmd", "git.exe"] - - out, rc = run_command(GITS, ["rev-parse", "--git-dir"], cwd=root, hide_stderr=True) - if rc != 0: - if verbose: - print("Directory %s not under git control" % root) - raise NotThisMethod("'git rev-parse --git-dir' returned error") - - # if there is a tag matching tag_prefix, this yields TAG-NUM-gHEX[-dirty] - # if there isn't one, this yields HEX[-dirty] (no NUM) - describe_out, rc = run_command( - GITS, - [ - "describe", - "--tags", - "--dirty", - "--always", - "--long", - "--match", - "%s*" % tag_prefix, - ], - cwd=root, - ) - # --long was added in git-1.5.5 - if describe_out is None: - raise NotThisMethod("'git describe' failed") - describe_out = describe_out.strip() - full_out, rc = run_command(GITS, ["rev-parse", "HEAD"], cwd=root) - if full_out is None: - raise NotThisMethod("'git rev-parse' failed") - full_out = full_out.strip() - - pieces = {} - pieces["long"] = full_out - pieces["short"] = full_out[:7] # maybe improved later - pieces["error"] = None - - # parse describe_out. It will be like TAG-NUM-gHEX[-dirty] or HEX[-dirty] - # TAG might have hyphens. - git_describe = describe_out - - # look for -dirty suffix - dirty = git_describe.endswith("-dirty") - pieces["dirty"] = dirty - if dirty: - git_describe = git_describe[: git_describe.rindex("-dirty")] - - # now we have TAG-NUM-gHEX or HEX - - if "-" in git_describe: - # TAG-NUM-gHEX - mo = re.search(r"^(.+)-(\d+)-g([0-9a-f]+)$", git_describe) - if not mo: - # unparseable. Maybe git-describe is misbehaving? - pieces["error"] = "unable to parse git-describe output: '%s'" % describe_out - return pieces - - # tag - full_tag = mo.group(1) - if not full_tag.startswith(tag_prefix): - if verbose: - fmt = "tag '%s' doesn't start with prefix '%s'" - print(fmt % (full_tag, tag_prefix)) - pieces["error"] = "tag '%s' doesn't start with prefix '%s'" % ( - full_tag, - tag_prefix, - ) - return pieces - pieces["closest-tag"] = full_tag[len(tag_prefix) :] - - # distance: number of commits since tag - pieces["distance"] = int(mo.group(2)) - - # commit: short hex revision ID - pieces["short"] = mo.group(3) - - else: - # HEX: no tags - pieces["closest-tag"] = None - count_out, rc = run_command(GITS, ["rev-list", "HEAD", "--count"], cwd=root) - pieces["distance"] = int(count_out) # total number of commits - - # commit date: see ISO-8601 comment in git_versions_from_keywords() - date = run_command(GITS, ["show", "-s", "--format=%ci", "HEAD"], cwd=root)[ - 0 - ].strip() - pieces["date"] = date.strip().replace(" ", "T", 1).replace(" ", "", 1) - - return pieces - - -def do_vcs_install(manifest_in, versionfile_source, ipy): - """Git-specific installation logic for Versioneer. - - For Git, this means creating/changing .gitattributes to mark _version.py - for export-subst keyword substitution. - """ - GITS = ["git"] - if sys.platform == "win32": - GITS = ["git.cmd", "git.exe"] - files = [manifest_in, versionfile_source] - if ipy: - files.append(ipy) - try: - me = __file__ - if me.endswith(".pyc") or me.endswith(".pyo"): - me = os.path.splitext(me)[0] + ".py" - versioneer_file = os.path.relpath(me) - except NameError: - versioneer_file = "versioneer.py" - files.append(versioneer_file) - present = False - try: - f = open(".gitattributes", "r") - for line in f.readlines(): - if line.strip().startswith(versionfile_source): - if "export-subst" in line.strip().split()[1:]: - present = True - f.close() - except EnvironmentError: - pass - if not present: - f = open(".gitattributes", "a+") - f.write("%s export-subst\n" % versionfile_source) - f.close() - files.append(".gitattributes") - run_command(GITS, ["add", "--"] + files) - - -def versions_from_parentdir(parentdir_prefix, root, verbose): - """Try to determine the version from the parent directory name. - - Source tarballs conventionally unpack into a directory that includes both - the project name and a version string. We will also support searching up - two directory levels for an appropriately named parent directory - """ - rootdirs = [] - - for i in range(3): - dirname = os.path.basename(root) - if dirname.startswith(parentdir_prefix): - return { - "version": dirname[len(parentdir_prefix) :], - "full-revisionid": None, - "dirty": False, - "error": None, - "date": None, - } - else: - rootdirs.append(root) - root = os.path.dirname(root) # up a level - - if verbose: - print( - "Tried directories %s but none started with prefix %s" - % (str(rootdirs), parentdir_prefix) - ) - raise NotThisMethod("rootdir doesn't start with parentdir_prefix") - - -SHORT_VERSION_PY = """ -# This file was generated by 'versioneer.py' (0.18) from -# revision-control system data, or from the parent directory name of an -# unpacked source archive. Distribution tarballs contain a pre-generated copy -# of this file. - -import json - -version_json = ''' -%s -''' # END VERSION_JSON - - -def get_versions(): - return json.loads(version_json) -""" - - -def versions_from_file(filename): - """Try to determine the version from _version.py if present.""" - try: - with open(filename) as f: - contents = f.read() - except EnvironmentError: - raise NotThisMethod("unable to read _version.py") - mo = re.search( - r"version_json = '''\n(.*)''' # END VERSION_JSON", contents, re.M | re.S - ) - if not mo: - mo = re.search( - r"version_json = '''\r\n(.*)''' # END VERSION_JSON", contents, re.M | re.S - ) - if not mo: - raise NotThisMethod("no version_json in _version.py") - return json.loads(mo.group(1)) - - -def write_to_version_file(filename, versions): - """Write the given version number to the given _version.py file.""" - os.unlink(filename) - contents = json.dumps(versions, sort_keys=True, indent=1, separators=(",", ": ")) - with open(filename, "w") as f: - f.write(SHORT_VERSION_PY % contents) - - print("set %s to '%s'" % (filename, versions["version"])) - - -def plus_or_dot(pieces): - """Return a + if we don't already have one, else return a .""" - if "+" in pieces.get("closest-tag", ""): - return "." - return "+" - - -def render_pep440(pieces): - """Build up version string, with post-release "local version identifier". - - Our goal: TAG[+DISTANCE.gHEX[.dirty]] . Note that if you - get a tagged build and then dirty it, you'll get TAG+0.gHEX.dirty - - Exceptions: - 1: no tags. git_describe was just HEX. 0+untagged.DISTANCE.gHEX[.dirty] - """ - if pieces["closest-tag"]: - rendered = pieces["closest-tag"] - if pieces["distance"] or pieces["dirty"]: - rendered += plus_or_dot(pieces) - rendered += "%d.g%s" % (pieces["distance"], pieces["short"]) - if pieces["dirty"]: - rendered += ".dirty" - else: - # exception #1 - rendered = "0+untagged.%d.g%s" % (pieces["distance"], pieces["short"]) - if pieces["dirty"]: - rendered += ".dirty" - return rendered - - -def render_pep440_pre(pieces): - """TAG[.post.devDISTANCE] -- No -dirty. - - Exceptions: - 1: no tags. 0.post.devDISTANCE - """ - if pieces["closest-tag"]: - rendered = pieces["closest-tag"] - if pieces["distance"]: - rendered += ".post.dev%d" % pieces["distance"] - else: - # exception #1 - rendered = "0.post.dev%d" % pieces["distance"] - return rendered - - -def render_pep440_post(pieces): - """TAG[.postDISTANCE[.dev0]+gHEX] . - - The ".dev0" means dirty. Note that .dev0 sorts backwards - (a dirty tree will appear "older" than the corresponding clean one), - but you shouldn't be releasing software with -dirty anyways. - - Exceptions: - 1: no tags. 0.postDISTANCE[.dev0] - """ - if pieces["closest-tag"]: - rendered = pieces["closest-tag"] - if pieces["distance"] or pieces["dirty"]: - rendered += ".post%d" % pieces["distance"] - if pieces["dirty"]: - rendered += ".dev0" - rendered += plus_or_dot(pieces) - rendered += "g%s" % pieces["short"] - else: - # exception #1 - rendered = "0.post%d" % pieces["distance"] - if pieces["dirty"]: - rendered += ".dev0" - rendered += "+g%s" % pieces["short"] - return rendered - - -def render_pep440_old(pieces): - """TAG[.postDISTANCE[.dev0]] . - - The ".dev0" means dirty. - - Eexceptions: - 1: no tags. 0.postDISTANCE[.dev0] - """ - if pieces["closest-tag"]: - rendered = pieces["closest-tag"] - if pieces["distance"] or pieces["dirty"]: - rendered += ".post%d" % pieces["distance"] - if pieces["dirty"]: - rendered += ".dev0" - else: - # exception #1 - rendered = "0.post%d" % pieces["distance"] - if pieces["dirty"]: - rendered += ".dev0" - return rendered - - -def render_git_describe(pieces): - """TAG[-DISTANCE-gHEX][-dirty]. - - Like 'git describe --tags --dirty --always'. - - Exceptions: - 1: no tags. HEX[-dirty] (note: no 'g' prefix) - """ - if pieces["closest-tag"]: - rendered = pieces["closest-tag"] - if pieces["distance"]: - rendered += "-%d-g%s" % (pieces["distance"], pieces["short"]) - else: - # exception #1 - rendered = pieces["short"] - if pieces["dirty"]: - rendered += "-dirty" - return rendered - - -def render_git_describe_long(pieces): - """TAG-DISTANCE-gHEX[-dirty]. - - Like 'git describe --tags --dirty --always -long'. - The distance/hash is unconditional. - - Exceptions: - 1: no tags. HEX[-dirty] (note: no 'g' prefix) - """ - if pieces["closest-tag"]: - rendered = pieces["closest-tag"] - rendered += "-%d-g%s" % (pieces["distance"], pieces["short"]) - else: - # exception #1 - rendered = pieces["short"] - if pieces["dirty"]: - rendered += "-dirty" - return rendered - - -def render(pieces, style): - """Render the given version pieces into the requested style.""" - if pieces["error"]: - return { - "version": "unknown", - "full-revisionid": pieces.get("long"), - "dirty": None, - "error": pieces["error"], - "date": None, - } - - if not style or style == "default": - style = "pep440" # the default - - if style == "pep440": - rendered = render_pep440(pieces) - elif style == "pep440-pre": - rendered = render_pep440_pre(pieces) - elif style == "pep440-post": - rendered = render_pep440_post(pieces) - elif style == "pep440-old": - rendered = render_pep440_old(pieces) - elif style == "git-describe": - rendered = render_git_describe(pieces) - elif style == "git-describe-long": - rendered = render_git_describe_long(pieces) - else: - raise ValueError("unknown style '%s'" % style) - - return { - "version": rendered, - "full-revisionid": pieces["long"], - "dirty": pieces["dirty"], - "error": None, - "date": pieces.get("date"), - } - - -class VersioneerBadRootError(Exception): - """The project root directory is unknown or missing key files.""" - - -def get_versions(verbose=False): - """Get the project version from whatever source is available. - - Returns dict with two keys: 'version' and 'full'. - """ - if "versioneer" in sys.modules: - # see the discussion in cmdclass.py:get_cmdclass() - del sys.modules["versioneer"] - - root = get_root() - cfg = get_config_from_root(root) - - assert cfg.VCS is not None, "please set [versioneer]VCS= in setup.cfg" - handlers = HANDLERS.get(cfg.VCS) - assert handlers, "unrecognized VCS '%s'" % cfg.VCS - verbose = verbose or cfg.verbose - assert ( - cfg.versionfile_source is not None - ), "please set versioneer.versionfile_source" - assert cfg.tag_prefix is not None, "please set versioneer.tag_prefix" - - versionfile_abs = os.path.join(root, cfg.versionfile_source) - - # extract version from first of: _version.py, VCS command (e.g. 'git - # describe'), parentdir. This is meant to work for developers using a - # source checkout, for users of a tarball created by 'setup.py sdist', - # and for users of a tarball/zipball created by 'git archive' or github's - # download-from-tag feature or the equivalent in other VCSes. - - get_keywords_f = handlers.get("get_keywords") - from_keywords_f = handlers.get("keywords") - if get_keywords_f and from_keywords_f: - try: - keywords = get_keywords_f(versionfile_abs) - ver = from_keywords_f(keywords, cfg.tag_prefix, verbose) - if verbose: - print("got version from expanded keyword %s" % ver) - return ver - except NotThisMethod: - pass - - try: - ver = versions_from_file(versionfile_abs) - if verbose: - print("got version from file %s %s" % (versionfile_abs, ver)) - return ver - except NotThisMethod: - pass - - from_vcs_f = handlers.get("pieces_from_vcs") - if from_vcs_f: - try: - pieces = from_vcs_f(cfg.tag_prefix, root, verbose) - ver = render(pieces, cfg.style) - if verbose: - print("got version from VCS %s" % ver) - return ver - except NotThisMethod: - pass - - try: - if cfg.parentdir_prefix: - ver = versions_from_parentdir(cfg.parentdir_prefix, root, verbose) - if verbose: - print("got version from parentdir %s" % ver) - return ver - except NotThisMethod: - pass - - if verbose: - print("unable to compute version") - - return { - "version": "0+unknown", - "full-revisionid": None, - "dirty": None, - "error": "unable to compute version", - "date": None, - } - - -def get_version(): - """Get the short version string for this project.""" - return get_versions()["version"] - - -def get_cmdclass(): - """Get the custom setuptools/distutils subclasses used by Versioneer.""" - if "versioneer" in sys.modules: - del sys.modules["versioneer"] - # this fixes the "python setup.py develop" case (also 'install' and - # 'easy_install .'), in which subdependencies of the main project are - # built (using setup.py bdist_egg) in the same python process. Assume - # a main project A and a dependency B, which use different versions - # of Versioneer. A's setup.py imports A's Versioneer, leaving it in - # sys.modules by the time B's setup.py is executed, causing B to run - # with the wrong versioneer. Setuptools wraps the sub-dep builds in a - # sandbox that restores sys.modules to it's pre-build state, so the - # parent is protected against the child's "import versioneer". By - # removing ourselves from sys.modules here, before the child build - # happens, we protect the child from the parent's versioneer too. - # Also see https://github.com/warner/python-versioneer/issues/52 - - cmds = {} - - # we add "version" to both distutils and setuptools - from distutils.core import Command - - class cmd_version(Command): - description = "report generated version string" - user_options = [] - boolean_options = [] - - def initialize_options(self): - pass - - def finalize_options(self): - pass - - def run(self): - vers = get_versions(verbose=True) - print("Version: %s" % vers["version"]) - print(" full-revisionid: %s" % vers.get("full-revisionid")) - print(" dirty: %s" % vers.get("dirty")) - print(" date: %s" % vers.get("date")) - if vers["error"]: - print(" error: %s" % vers["error"]) - - cmds["version"] = cmd_version - - # we override "build_py" in both distutils and setuptools - # - # most invocation pathways end up running build_py: - # distutils/build -> build_py - # distutils/install -> distutils/build ->.. - # setuptools/bdist_wheel -> distutils/install ->.. - # setuptools/bdist_egg -> distutils/install_lib -> build_py - # setuptools/install -> bdist_egg ->.. - # setuptools/develop -> ? - # pip install: - # copies source tree to a tempdir before running egg_info/etc - # if .git isn't copied too, 'git describe' will fail - # then does setup.py bdist_wheel, or sometimes setup.py install - # setup.py egg_info -> ? - - # we override different "build_py" commands for both environments - if "setuptools" in sys.modules: - from setuptools.command.build_py import build_py as _build_py - else: - from distutils.command.build_py import build_py as _build_py - - class cmd_build_py(_build_py): - def run(self): - root = get_root() - cfg = get_config_from_root(root) - versions = get_versions() - _build_py.run(self) - # now locate _version.py in the new build/ directory and replace - # it with an updated value - if cfg.versionfile_build: - target_versionfile = os.path.join(self.build_lib, cfg.versionfile_build) - print("UPDATING %s" % target_versionfile) - write_to_version_file(target_versionfile, versions) - - cmds["build_py"] = cmd_build_py - - if "cx_Freeze" in sys.modules: # cx_freeze enabled? - from cx_Freeze.dist import build_exe as _build_exe - - # nczeczulin reports that py2exe won't like the pep440-style string - # as FILEVERSION, but it can be used for PRODUCTVERSION, e.g. - # setup(console=[{ - # "version": versioneer.get_version().split("+", 1)[0], # FILEVERSION - # "product_version": versioneer.get_version(), - # ... - - class cmd_build_exe(_build_exe): - def run(self): - root = get_root() - cfg = get_config_from_root(root) - versions = get_versions() - target_versionfile = cfg.versionfile_source - print("UPDATING %s" % target_versionfile) - write_to_version_file(target_versionfile, versions) - - _build_exe.run(self) - os.unlink(target_versionfile) - with open(cfg.versionfile_source, "w") as f: - LONG = LONG_VERSION_PY[cfg.VCS] - f.write( - LONG - % { - "DOLLAR": "$", - "STYLE": cfg.style, - "TAG_PREFIX": cfg.tag_prefix, - "PARENTDIR_PREFIX": cfg.parentdir_prefix, - "VERSIONFILE_SOURCE": cfg.versionfile_source, - } - ) - - cmds["build_exe"] = cmd_build_exe - del cmds["build_py"] - - if "py2exe" in sys.modules: # py2exe enabled? - try: - from py2exe.distutils_buildexe import py2exe as _py2exe # py3 - except ImportError: - from py2exe.build_exe import py2exe as _py2exe # py2 - - class cmd_py2exe(_py2exe): - def run(self): - root = get_root() - cfg = get_config_from_root(root) - versions = get_versions() - target_versionfile = cfg.versionfile_source - print("UPDATING %s" % target_versionfile) - write_to_version_file(target_versionfile, versions) - - _py2exe.run(self) - os.unlink(target_versionfile) - with open(cfg.versionfile_source, "w") as f: - LONG = LONG_VERSION_PY[cfg.VCS] - f.write( - LONG - % { - "DOLLAR": "$", - "STYLE": cfg.style, - "TAG_PREFIX": cfg.tag_prefix, - "PARENTDIR_PREFIX": cfg.parentdir_prefix, - "VERSIONFILE_SOURCE": cfg.versionfile_source, - } - ) - - cmds["py2exe"] = cmd_py2exe - - # we override different "sdist" commands for both environments - if "setuptools" in sys.modules: - from setuptools.command.sdist import sdist as _sdist - else: - from distutils.command.sdist import sdist as _sdist - - class cmd_sdist(_sdist): - def run(self): - versions = get_versions() - self._versioneer_generated_versions = versions - # unless we update this, the command will keep using the old - # version - self.distribution.metadata.version = versions["version"] - return _sdist.run(self) - - def make_release_tree(self, base_dir, files): - root = get_root() - cfg = get_config_from_root(root) - _sdist.make_release_tree(self, base_dir, files) - # now locate _version.py in the new base_dir directory - # (remembering that it may be a hardlink) and replace it with an - # updated value - target_versionfile = os.path.join(base_dir, cfg.versionfile_source) - print("UPDATING %s" % target_versionfile) - write_to_version_file( - target_versionfile, self._versioneer_generated_versions - ) - - cmds["sdist"] = cmd_sdist - - return cmds - - -CONFIG_ERROR = """ -setup.cfg is missing the necessary Versioneer configuration. You need -a section like: - - [versioneer] - VCS = git - style = pep440 - versionfile_source = src/myproject/_version.py - versionfile_build = myproject/_version.py - tag_prefix = - parentdir_prefix = myproject- - -You will also need to edit your setup.py to use the results: - - import versioneer - setup(version=versioneer.get_version(), - cmdclass=versioneer.get_cmdclass(), ...) - -Please read the docstring in ./versioneer.py for configuration instructions, -edit setup.cfg, and re-run the installer or 'python versioneer.py setup'. -""" - -SAMPLE_CONFIG = """ -# See the docstring in versioneer.py for instructions. Note that you must -# re-run 'versioneer.py setup' after changing this section, and commit the -# resulting files. - -[versioneer] -#VCS = git -#style = pep440 -#versionfile_source = -#versionfile_build = -#tag_prefix = -#parentdir_prefix = - -""" - -INIT_PY_SNIPPET = """ -from ._version import get_versions -__version__ = get_versions()['version'] -del get_versions -""" - - -def do_setup(): - """Main VCS-independent setup function for installing Versioneer.""" - root = get_root() - try: - cfg = get_config_from_root(root) - except ( - EnvironmentError, - configparser.NoSectionError, - configparser.NoOptionError, - ) as e: - if isinstance(e, (EnvironmentError, configparser.NoSectionError)): - print("Adding sample versioneer config to setup.cfg", file=sys.stderr) - with open(os.path.join(root, "setup.cfg"), "a") as f: - f.write(SAMPLE_CONFIG) - print(CONFIG_ERROR, file=sys.stderr) - return 1 - - print(" creating %s" % cfg.versionfile_source) - with open(cfg.versionfile_source, "w") as f: - LONG = LONG_VERSION_PY[cfg.VCS] - f.write( - LONG - % { - "DOLLAR": "$", - "STYLE": cfg.style, - "TAG_PREFIX": cfg.tag_prefix, - "PARENTDIR_PREFIX": cfg.parentdir_prefix, - "VERSIONFILE_SOURCE": cfg.versionfile_source, - } - ) - - ipy = os.path.join(os.path.dirname(cfg.versionfile_source), "__init__.py") - if os.path.exists(ipy): - try: - with open(ipy, "r") as f: - old = f.read() - except EnvironmentError: - old = "" - if INIT_PY_SNIPPET not in old: - print(" appending to %s" % ipy) - with open(ipy, "a") as f: - f.write(INIT_PY_SNIPPET) - else: - print(" %s unmodified" % ipy) - else: - print(" %s doesn't exist, ok" % ipy) - ipy = None - - # Make sure both the top-level "versioneer.py" and versionfile_source - # (PKG/_version.py, used by runtime code) are in MANIFEST.in, so - # they'll be copied into source distributions. Pip won't be able to - # install the package without this. - manifest_in = os.path.join(root, "MANIFEST.in") - simple_includes = set() - try: - with open(manifest_in, "r") as f: - for line in f: - if line.startswith("include "): - for include in line.split()[1:]: - simple_includes.add(include) - except EnvironmentError: - pass - # That doesn't cover everything MANIFEST.in can do - # (http://docs.python.org/2/distutils/sourcedist.html#commands), so - # it might give some false negatives. Appending redundant 'include' - # lines is safe, though. - if "versioneer.py" not in simple_includes: - print(" appending 'versioneer.py' to MANIFEST.in") - with open(manifest_in, "a") as f: - f.write("include versioneer.py\n") - else: - print(" 'versioneer.py' already in MANIFEST.in") - if cfg.versionfile_source not in simple_includes: - print( - " appending versionfile_source ('%s') to MANIFEST.in" - % cfg.versionfile_source - ) - with open(manifest_in, "a") as f: - f.write("include %s\n" % cfg.versionfile_source) - else: - print(" versionfile_source already in MANIFEST.in") - - # Make VCS-specific changes. For git, this means creating/changing - # .gitattributes to mark _version.py for export-subst keyword - # substitution. - do_vcs_install(manifest_in, cfg.versionfile_source, ipy) - return 0 - - -def scan_setup_py(): - """Validate the contents of setup.py against Versioneer's expectations.""" - found = set() - setters = False - errors = 0 - with open("setup.py", "r") as f: - for line in f.readlines(): - if "import versioneer" in line: - found.add("import") - if "versioneer.get_cmdclass()" in line: - found.add("cmdclass") - if "versioneer.get_version()" in line: - found.add("get_version") - if "versioneer.VCS" in line: - setters = True - if "versioneer.versionfile_source" in line: - setters = True - if len(found) != 3: - print("") - print("Your setup.py appears to be missing some important items") - print("(but I might be wrong). Please make sure it has something") - print("roughly like the following:") - print("") - print(" import versioneer") - print(" setup( version=versioneer.get_version(),") - print(" cmdclass=versioneer.get_cmdclass(), ...)") - print("") - errors += 1 - if setters: - print("You should remove lines like 'versioneer.VCS = ' and") - print("'versioneer.versionfile_source = ' . This configuration") - print("now lives in setup.cfg, and should be removed from setup.py") - print("") - errors += 1 - return errors - - -if __name__ == "__main__": - cmd = sys.argv[1] - if cmd == "setup": - errors = do_setup() - errors += scan_setup_py() - if errors: - sys.exit(1)