Cloudfiles emj

.bumpversion.cfg

@@ -0,0 +1,8 @@
+[bumpversion]
+current_version = 0.1.0
+commit = True
+tag = True
+
+[bumpversion:file:skeleton_keys/__init__.py]
+
+[bumpversion:file:doc/source/conf.py]

.gitignore

@@ -57,6 +57,8 @@ coverage.xml
 
 # Sphinx documentation
 docs/_build/
+doc/build/
+doc/source/reference/generated/
 
 # PyBuilder
 target/

CONTRIBUTING.md

@@ -0,0 +1,26 @@
+# Allen Institute Contribution Agreement
+
+This document describes the terms under which you may make “Contributions” —
+which may include without limitation, software additions, revisions, bug fixes, configuration changes,
+documentation, or any other materials — to any of the projects owned or managed by the Allen Institute.
+If you have questions about these terms, please contact us at terms@alleninstitute.org.
+
+You certify that:
+
+•	Your Contributions are either:
+
+1.	Created in whole or in part by you and you have the right to submit them under the designated license
+(described below); or
+2.	Based upon previous work that, to the best of your knowledge, is covered under an appropriate
+open source license and you have the right under that license to submit that work with modifications,
+whether created in whole or in part by you, under the designated license; or
+
+3.	Provided directly to you by some other person who certified (1) or (2) and you have not modified them.
+
+•	You are granting your Contributions to the Allen Institute under the terms of the [2-Clause BSD license](https://opensource.org/licenses/BSD-2-Clause)
+(the “designated license”).
+
+•	You understand and agree that the Allen Institute projects and your Contributions are public and that
+a record of the Contributions (including all metadata and personal information you submit with them) is
+maintained indefinitely and may be redistributed consistent with the Allen Institute’s mission and the
+2-Clause BSD license.

Dockerfile

@@ -1,16 +1,25 @@
-FROM continuumio/miniconda3:4.10.3
-RUN apt-get update && apt-get install -y build-essential && rm -rf /var/lib/apt/lists/*
-RUN conda config --set channel_priority strict 
-RUN conda install -y -c conda-forge rtree==0.9.7 fenics==2019.1.0 python==3.8 mshr==2019.1.0 hdf5==1.10.6 h5py==2.10.0
-RUN pip install git+https://github.com/fcollman/AllenSDK.git
-RUN pip install git+https://github.com/AllenInstitute/neuron_morphology@cloudfiles
-ARG GITHUB_TOKEN
-WORKDIR /usr/local/src
-RUN git clone https://${GITHUB_TOKEN}@github.com/AllenInstitute/ccf_streamlines.git &&\
-    pip install ./ccf_streamlines &&\
-    rm -rf /usr/local/src/ccf_streamlines
-WORKDIR /usr/local/src/skeleton_keys
-COPY setup.cfg  /usr/local/src/skeleton_keys
-RUN python3 -c "import configparser; c = configparser.ConfigParser(); c.read('setup.cfg'); print(c['options']['install_requires'])" | xargs pip install
+FROM condaforge/mambaforge:4.9.2-5 as conda
+RUN apt-get update && \
+    apt-get install -y build-essential libglu1 \
+    libxcursor-dev libxft2 libxinerama1 \
+    libfltk1.3-dev libfreetype6-dev \
+    libgl1-mesa-dev  && \
+    rm -rf /var/lib/apt/lists/*
+RUN mamba install -y -c conda-forge conda-lock conda-pack
+COPY conda-lock.yml .
+RUN conda-lock install --name skeleton_keys conda-lock.yml
+SHELL ["mamba", "run","-n","skeleton_keys","/bin/bash", "-c"]
+COPY requirements.txt .
+RUN mamba run -n skeleton_keys pip install -r requirements.txt
 COPY . /usr/local/src/skeleton_keys
-RUN python setup.py install
+WORKDIR /usr/local/src/skeleton_keys
+RUN mamba run -n skeleton_keys pip install .
+# RUN conda-pack -n skeleton_keys -o /tmp/env.tar && \
+#     mkdir /venv && cd /venv && tar xf /tmp/env.tar && \
+#     rm /tmp/env.tar
+# FROM debian:buster AS runtime
+# COPY --from=conda /venv /venv
+# SHELL ["/bin/bash", "-c"]
+# ENTRYPOINT source /venv/bin/activate && \
+#     python --version
+# WORKDIR /usr/local/src/skeleton_keys

LICENSE

@@ -0,0 +1,33 @@
+Allen Institute Software License – This software license is the 2-clause BSD
+license plus a third clause that prohibits redistribution and use for
+commercial purposes without further permission.
+
+Copyright © 2022. Allen Institute.  All rights reserved.
+
+Redistribution and use in source and binary forms, with or without
+modification, are permitted provided that the following conditions are met:
+
+1. Redistributions of source code must retain the above copyright notice, this
+list of conditions and the following disclaimer.
+
+2. Redistributions in binary form must reproduce the above copyright notice,
+this list of conditions and the following disclaimer in the documentation
+and/or other materials provided with the distribution.
+
+3. Redistributions and use for commercial purposes are not permitted without
+the Allen Institute’s written permission. For purposes of this license,
+commercial purposes are the incorporation of the Allen Institute's software
+into anything for which you will charge fees or other compensation or use of
+the software to perform a commercial service for a third party. Contact
+terms@alleninstitute.org for commercial licensing opportunities.
+
+THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND
+ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED
+WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
+DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE
+FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL
+DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR
+SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER
+CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY,
+OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE
+OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.

README.md

@@ -3,6 +3,7 @@
 This package supports the skeletal analysis of morphologies.
 
 
+
 Installation instructions
 =========================
 
@@ -50,7 +51,9 @@ skelekeys-postprocess-features
 ------------------------------
 script to to take a long form set of features and post-process them to remove zeros and perform zscoring and/or uniform scaling of features.
 
-
+Statement of Support
+====================
+This code is an important part of the internal Allen Institute code base and we are actively using and maintaining it. Issues are encouraged, but because this tool is so central to our mission pull requests might not be accepted if they conflict with our existing plans.