From 4f32eaf76011198d94c11770fa7336a91b742a84 Mon Sep 17 00:00:00 2001 From: Joel Greer Date: Fri, 28 Jun 2024 11:19:08 +0100 Subject: [PATCH 1/9] Fixing pkg versions and version bump --- pyproject.toml | 26 +++++++++++++------------- 1 file changed, 13 insertions(+), 13 deletions(-) diff --git a/pyproject.toml b/pyproject.toml index d368385..233d4f8 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -1,31 +1,31 @@ [tool.poetry] name = "empiarreader" -version = "0.0.4" +version = "0.0.5" description = "EMPIARReader provides utilities to lazily load data from EMPIAR into a machine-learning-friendly dataset format or to locally download the files." authors = ["mooniean ", "ots22 "] readme = "README.md" [tool.poetry.dependencies] python = "^3.8" -intake = "^0.6.5" -bs4 = "^0.0.1" -matplotlib = "^3.6.1" -requests = "^2.28.1" -scikit-image = "^0.19.3" +intake = "0.6.6" +bs4 = "0.0.1" +matplotlib = "3.6.1" +requests = "2.28.1" +scikit-image = "0.19.3" xarray = "^2022.9.0" mrcfile = "^1.4.3" starfile = "^0.4.11" -intake-xarray = "^0.6.1" -aiohttp = "^3.8.3" -setuptools = "^67.7.2" -pre-commit = "^3.3.3" +intake-xarray = "0.6.1" +aiohttp = "3.8.3" +setuptools = "67.7.2" +pre-commit = "3.3.3" # Dependencies for 'extras' -Sphinx = { version = "^5.0", optional = true } -pydata-sphinx-theme = { version = "^0.7", optional = true } +Sphinx = { version = "4.5.0", optional = true } +pydata-sphinx-theme = { version = "0.7.2", optional = true } [tool.poetry.dev-dependencies] -pytest = "^6.2.5" +pytest = "6.2.5" [tool.poetry.extras] doc = ["Sphinx", "pydata-sphinx-theme"] From 4ec477107a1054baee5c89baef2aa633d828a258 Mon Sep 17 00:00:00 2001 From: Joel Greer Date: Fri, 28 Jun 2024 11:42:57 +0100 Subject: [PATCH 2/9] Fix numpy version --- pyproject.toml | 1 + 1 file changed, 1 insertion(+) diff --git a/pyproject.toml b/pyproject.toml index 233d4f8..faad447 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -19,6 +19,7 @@ intake-xarray = "0.6.1" aiohttp = "3.8.3" setuptools = "67.7.2" pre-commit = "3.3.3" +numpy = "1.23.3" # Dependencies for 'extras' Sphinx = { version = "4.5.0", optional = true } From 000f8c74d251aac50a218033ee30bcb23b2efb43 Mon Sep 17 00:00:00 2001 From: Joel Greer Date: Fri, 28 Jun 2024 13:09:49 +0100 Subject: [PATCH 3/9] Unfix others packages but fix numpy for xarr --- pyproject.toml | 24 ++++++++++++------------ 1 file changed, 12 insertions(+), 12 deletions(-) diff --git a/pyproject.toml b/pyproject.toml index faad447..fb35ba1 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -7,26 +7,26 @@ readme = "README.md" [tool.poetry.dependencies] python = "^3.8" -intake = "0.6.6" -bs4 = "0.0.1" -matplotlib = "3.6.1" -requests = "2.28.1" -scikit-image = "0.19.3" +intake = "^0.6.6" +bs4 = "^0.0.1" +matplotlib = "^3.6.1" +requests = "^2.28.1" +scikit-image = "^0.19.3" xarray = "^2022.9.0" mrcfile = "^1.4.3" starfile = "^0.4.11" -intake-xarray = "0.6.1" -aiohttp = "3.8.3" -setuptools = "67.7.2" -pre-commit = "3.3.3" +intake-xarray = "^0.6.1" +aiohttp = "^3.8.3" +setuptools = "^67.7.2" +pre-commit = "^3.3.3" numpy = "1.23.3" # Dependencies for 'extras' -Sphinx = { version = "4.5.0", optional = true } -pydata-sphinx-theme = { version = "0.7.2", optional = true } +Sphinx = { version = "^4.5.0", optional = true } +pydata-sphinx-theme = { version = "^0.7", optional = true } [tool.poetry.dev-dependencies] -pytest = "6.2.5" +pytest = "^6.2.5" [tool.poetry.extras] doc = ["Sphinx", "pydata-sphinx-theme"] From b6dd48cb829ea1ac2e878f5fcb73d5efd262a3c2 Mon Sep 17 00:00:00 2001 From: Joel Greer Date: Fri, 28 Jun 2024 13:10:18 +0100 Subject: [PATCH 4/9] version bump --- pyproject.toml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/pyproject.toml b/pyproject.toml index fb35ba1..9695380 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -1,6 +1,6 @@ [tool.poetry] name = "empiarreader" -version = "0.0.5" +version = "0.0.6" description = "EMPIARReader provides utilities to lazily load data from EMPIAR into a machine-learning-friendly dataset format or to locally download the files." authors = ["mooniean ", "ots22 "] readme = "README.md" From 69c25f66302fe26a49cfd8b6c5688a5fe9213a67 Mon Sep 17 00:00:00 2001 From: Joel Greer Date: Wed, 19 Feb 2025 14:59:17 +0000 Subject: [PATCH 5/9] Version bump to test new repo testpypi workflow --- pyproject.toml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/pyproject.toml b/pyproject.toml index 9695380..644e66d 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -1,6 +1,6 @@ [tool.poetry] name = "empiarreader" -version = "0.0.6" +version = "0.0.7" description = "EMPIARReader provides utilities to lazily load data from EMPIAR into a machine-learning-friendly dataset format or to locally download the files." authors = ["mooniean ", "ots22 "] readme = "README.md" From a56e047fe2ae048ce5efd2b6dbe3a3777640e1df Mon Sep 17 00:00:00 2001 From: Joel Greer Date: Mon, 19 May 2025 11:59:00 +0100 Subject: [PATCH 6/9] updated pypi workflows and version bump --- .github/workflows/python-publish.yml | 8 ++++---- pyproject.toml | 2 +- 2 files changed, 5 insertions(+), 5 deletions(-) diff --git a/.github/workflows/python-publish.yml b/.github/workflows/python-publish.yml index 6086ef1..405df2f 100644 --- a/.github/workflows/python-publish.yml +++ b/.github/workflows/python-publish.yml @@ -22,7 +22,7 @@ jobs: - name: build-bin-whl run: python3 -m build - name: grab-build - uses: actions/upload-artifact@v3 + uses: actions/upload-artifact@v4 with: name: pkg-dist path: dist/ @@ -42,7 +42,7 @@ jobs: steps: - name: download-dists - uses: actions/download-artifact@v3 + uses: actions/download-artifact@v4 with: name: pkg-dist path: dist/ @@ -62,7 +62,7 @@ jobs: steps: - name: download-dists - uses: actions/download-artifact@v3 + uses: actions/download-artifact@v4 with: name: pkg-dist path: dist/ @@ -104,7 +104,7 @@ jobs: steps: - name: download-dists - uses: actions/download-artifact@v3 + uses: actions/download-artifact@v4 with: name: pkg-dist path: dist/ diff --git a/pyproject.toml b/pyproject.toml index d368385..4473b33 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -1,6 +1,6 @@ [tool.poetry] name = "empiarreader" -version = "0.0.4" +version = "0.0.5" description = "EMPIARReader provides utilities to lazily load data from EMPIAR into a machine-learning-friendly dataset format or to locally download the files." authors = ["mooniean ", "ots22 "] readme = "README.md" From 78afc6d0937e7d78b2468b0da6331d837393283e Mon Sep 17 00:00:00 2001 From: Joel Greer Date: Mon, 19 May 2025 12:03:59 +0100 Subject: [PATCH 7/9] updating workflows --- .github/workflows/draft-pdf.yml | 2 +- pyproject.toml | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/.github/workflows/draft-pdf.yml b/.github/workflows/draft-pdf.yml index 8effae6..f24d0d0 100644 --- a/.github/workflows/draft-pdf.yml +++ b/.github/workflows/draft-pdf.yml @@ -6,7 +6,7 @@ jobs: name: Paper Draft steps: - name: Checkout - uses: actions/checkout@v3 + uses: actions/checkout@v4 - name: Build draft PDF uses: openjournals/openjournals-draft-action@master with: diff --git a/pyproject.toml b/pyproject.toml index 469d6dc..c80dc8d 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -1,6 +1,6 @@ [tool.poetry] name = "empiarreader" -version = "0.0.8" +version = "0.0.9" description = "EMPIARReader provides utilities to lazily load data from EMPIAR into a machine-learning-friendly dataset format or to locally download the files." authors = ["mooniean ", "ots22 "] readme = "README.md" From abb27af5383c215ac73c076c8085be17acc9ac92 Mon Sep 17 00:00:00 2001 From: Joel Greer Date: Mon, 19 May 2025 12:06:43 +0100 Subject: [PATCH 8/9] Updating workflows --- .github/workflows/draft-pdf.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/draft-pdf.yml b/.github/workflows/draft-pdf.yml index f24d0d0..1b11ba9 100644 --- a/.github/workflows/draft-pdf.yml +++ b/.github/workflows/draft-pdf.yml @@ -14,7 +14,7 @@ jobs: # This should be the path to the paper within your repo. paper-path: joss/paper.md - name: Upload - uses: actions/upload-artifact@v1 + uses: actions/upload-artifact@v4 with: name: paper # This is the output path where Pandoc will write the compiled From 1627e86971b8bc650d5488285a60e6fe70805c0f Mon Sep 17 00:00:00 2001 From: Joel Greer Date: Mon, 19 May 2025 12:07:03 +0100 Subject: [PATCH 9/9] version bump --- pyproject.toml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/pyproject.toml b/pyproject.toml index c80dc8d..2790614 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -1,6 +1,6 @@ [tool.poetry] name = "empiarreader" -version = "0.0.9" +version = "0.0.10" description = "EMPIARReader provides utilities to lazily load data from EMPIAR into a machine-learning-friendly dataset format or to locally download the files." authors = ["mooniean ", "ots22 "] readme = "README.md"