diff --git a/.github/workflows/publish.yaml b/.github/workflows/publish.yaml index 46f785eab3..c7ed45737c 100644 --- a/.github/workflows/publish.yaml +++ b/.github/workflows/publish.yaml @@ -24,7 +24,6 @@ jobs: - name: Install dependencies run: | pip install devpi-client - pip install hatch - name: Authenticate and upload to devpi run: | @@ -41,6 +40,36 @@ jobs: pip install hatch echo "version=$(hatch version)" >> "$GITHUB_OUTPUT" + publish-packages: + runs-on: ubuntu-latest + + strategy: + matrix: + package: [napari-bbox, napari-spfluo, scipion-app, scipion-fluo, scipion-fluo-singleparticle, scipion-pyworkflow, spfluo] + + steps: + - name: Checkout code + uses: actions/checkout@v4 + + - name: Set up Python + uses: actions/setup-python@v5 + with: + python-version: '3.11' + + - name: Install dependencies + run: | + pip install devpi-client + + - name: Authenticate and upload to devpi + run: | + cd packages/${{ matrix.package }} + devpi use https://pypi.spfluo.ovh + devpi login jean --password=${{ secrets.DEVPI_PASSWORD }} + devpi use jean/dev + devpi upload + env: + DEVPI_PASSWORD: ${{ secrets.DEVPI_PASSWORD }} + compile-requirements: runs-on: ubuntu-latest needs: publish @@ -50,7 +79,7 @@ jobs: matrix: platform: [x86_64-unknown-linux-gnu, x86_64-pc-windows-msvc] gpu: [false, true] - python_version: ["8", "9", "10", "11", "12"] + python_version: ["9", "10", "11", "12"] steps: - name: Checkout repository @@ -60,7 +89,6 @@ jobs: uses: actions/setup-python@v5 with: python-version: | - 3.8 3.9 3.10 3.11 @@ -100,9 +128,8 @@ jobs: --python-version 3.${{ matrix.python_version }} --python-platform ${{ matrix.platform }} -c constraints.txt - --extra=gpu --emit-index-url - --index-url https://pypi.spfluo.ovh/jean/dev-pytorch-cu124/+simple/ # pytorch is in the deps of spfluo-app[gpu], so we need a custom index + --index-url https://pypi.spfluo.ovh/jean/dev-pytorch-cu124/+simple/ # torch is in the deps we need a custom index to enable CUDA - name: Append to requirements spfluo-app run: | diff --git a/packages/napari-bbox/.github/workflows/devpi.yaml b/packages/napari-bbox/.github/workflows/devpi.yaml deleted file mode 100644 index 8592419596..0000000000 --- a/packages/napari-bbox/.github/workflows/devpi.yaml +++ /dev/null @@ -1,32 +0,0 @@ -name: Publish on Tag - -on: - push: - tags: - - '*' - -jobs: - publish: - runs-on: ubuntu-latest - - steps: - - name: Checkout code - uses: actions/checkout@v4 - - - name: Set up Python - uses: actions/setup-python@v4 - with: - python-version: '3.10' # Replace with your desired Python version - - - name: Install dependencies - run: | - pip install devpi-client # Install devpi-client - - - name: Authenticate and upload to devpi - run: | - devpi use https://pypi.spfluo.ovh - devpi login jean --password=${{ secrets.DEVPI_PASSWORD }} - devpi use jean/dev - devpi upload - env: - DEVPI_PASSWORD: ${{ secrets.DEVPI_PASSWORD }} \ No newline at end of file diff --git a/packages/napari-spfluo/.github/workflows/devpi.yaml b/packages/napari-spfluo/.github/workflows/devpi.yaml deleted file mode 100644 index fb2fb603c4..0000000000 --- a/packages/napari-spfluo/.github/workflows/devpi.yaml +++ /dev/null @@ -1,32 +0,0 @@ -name: Publish on Tag - -on: - push: - tags: - - '*' - -jobs: - publish: - runs-on: ubuntu-latest - - steps: - - name: Checkout code - uses: actions/checkout@v4 - - - name: Set up Python - uses: actions/setup-python@v4 - with: - python-version: '3.10' # Replace with your desired Python version - - - name: Install dependencies - run: | - pip install devpi-client # Install devpi-client - - - name: Authenticate and upload to devpi - run: | - devpi use https://pypi.spfluo.ovh - devpi login jean --password=${{ secrets.DEVPI_PASSWORD }} - devpi use jean/dev - devpi upload - env: - DEVPI_PASSWORD: ${{ secrets.DEVPI_PASSWORD }} diff --git a/packages/napari-spfluo/hatch.toml b/packages/napari-spfluo/hatch.toml index 2b3f6d73ac..67e7b4da51 100644 --- a/packages/napari-spfluo/hatch.toml +++ b/packages/napari-spfluo/hatch.toml @@ -1,5 +1,6 @@ [version] source = "vcs" +raw-options = { root = "../.." } [build.hooks.vcs] version-file = "src/napari_spfluo/_version.py" diff --git a/packages/napari-spfluo/pyproject.toml b/packages/napari-spfluo/pyproject.toml index 9f199ee6e9..95baccc2fc 100644 --- a/packages/napari-spfluo/pyproject.toml +++ b/packages/napari-spfluo/pyproject.toml @@ -4,7 +4,7 @@ build-backend = "hatchling.build" [project] name = "napari-spfluo" -version = "0.0.1" +dynamic = ["version"] description = "A plugin to use spfluo within napari" readme = "README.md" license = "MIT" @@ -59,4 +59,4 @@ line-length = 79 target-version = ['py39', 'py310', 'py311'] [tool.uv.sources] -spfluo = {workspace = true} \ No newline at end of file +spfluo = {path = "../spfluo"} \ No newline at end of file diff --git a/packages/scipion-app/.github/workflows/devpi.yaml b/packages/scipion-app/.github/workflows/devpi.yaml deleted file mode 100644 index 433658a91f..0000000000 --- a/packages/scipion-app/.github/workflows/devpi.yaml +++ /dev/null @@ -1,32 +0,0 @@ -name: Publish on Tag - -on: - push: - tags: - - '*' - -jobs: - publish: - runs-on: ubuntu-latest - - steps: - - name: Checkout code - uses: actions/checkout@v4 - - - name: Set up Python - uses: actions/setup-python@v4 - with: - python-version: '3.10' - - - name: Install dependencies - run: | - pip install devpi-client # Install devpi-client - - - name: Authenticate and upload to devpi - run: | - devpi use https://pypi.spfluo.ovh - devpi login jean --password=${{ secrets.DEVPI_PASSWORD }} - devpi use jean/dev - devpi upload - env: - DEVPI_PASSWORD: ${{ secrets.DEVPI_PASSWORD }} diff --git a/packages/scipion-app/pyproject.toml b/packages/scipion-app/pyproject.toml index f1979d1cea..bfa34eb911 100644 --- a/packages/scipion-app/pyproject.toml +++ b/packages/scipion-app/pyproject.toml @@ -40,4 +40,4 @@ guiplugin = "scipion.guiplugin" "scipion" = ["templates/*.template", "templates/*.json"] [tool.uv.sources] -scipion-fluo = {workspace = true} \ No newline at end of file +scipion-fluo = {path = "../scipion-fluo"} \ No newline at end of file diff --git a/packages/scipion-fluo-singleparticle/.github/workflows/devpi.yaml b/packages/scipion-fluo-singleparticle/.github/workflows/devpi.yaml deleted file mode 100644 index bb2ad5b532..0000000000 --- a/packages/scipion-fluo-singleparticle/.github/workflows/devpi.yaml +++ /dev/null @@ -1,38 +0,0 @@ -name: Publish on Tag - -on: - push: - tags: - - '*' - -jobs: - publish: - runs-on: ubuntu-latest - - steps: - - name: Checkout code - uses: actions/checkout@v4 - - - name: Set up Python - uses: actions/setup-python@v4 - with: - python-version: '3.10' - - - name: Install dependencies - run: | - pip install devpi-client # Install devpi-client - - - name: Set up Java - uses: actions/setup-java@v3 - with: - distribution: 'temurin' - java-version: '8' - - - name: Authenticate and upload to devpi - run: | - devpi use https://pypi.spfluo.ovh - devpi login jean --password=${{ secrets.DEVPI_PASSWORD }} - devpi use jean/dev - devpi upload - env: - DEVPI_PASSWORD: ${{ secrets.DEVPI_PASSWORD }} diff --git a/packages/scipion-fluo-singleparticle/hatch.toml b/packages/scipion-fluo-singleparticle/hatch.toml index a2ea8fd645..4f757bbfaa 100644 --- a/packages/scipion-fluo-singleparticle/hatch.toml +++ b/packages/scipion-fluo-singleparticle/hatch.toml @@ -1,9 +1,12 @@ [version] source = "vcs" +raw-options = { root = "../.." } [build.targets.sdist] exclude = [ "/.github", + "/.gitignore", + "/.pre-commit-config.yaml", ] [build.targets.wheel] diff --git a/packages/scipion-fluo-singleparticle/pyproject.toml b/packages/scipion-fluo-singleparticle/pyproject.toml index 6282f8f2c9..d15fdaa32c 100644 --- a/packages/scipion-fluo-singleparticle/pyproject.toml +++ b/packages/scipion-fluo-singleparticle/pyproject.toml @@ -8,7 +8,7 @@ description = "Scipion plugin for single particle reconstruction." readme = "README.rst" authors = [{name = "Jean Plumail", email = "jplumail@unistra.fr"}] keywords = ["scipion", "fluorescence", "imageprocessing", "scipion-3.0"] -version = "0.0.1" +dynamic = ["version"] dependencies = [ "scipion-pyworkflow", "scipion-fluo", @@ -27,7 +27,7 @@ Repository = "https://github.com/jplumail/scipion-fluo-singleparticle" singleparticle = "singleparticle" [tool.uv.sources] -scipion-pyworkflow = {workspace=true} -scipion-fluo = {workspace=true} -spfluo = {workspace=true} -napari-spfluo = {workspace=true} \ No newline at end of file +scipion-pyworkflow = {path="../scipion-pyworkflow"} +scipion-fluo = {path="../scipion-fluo"} +spfluo = {path="../spfluo"} +napari-spfluo = {path="../napari-spfluo"} \ No newline at end of file diff --git a/packages/scipion-fluo/.github/workflows/devpi.yaml b/packages/scipion-fluo/.github/workflows/devpi.yaml deleted file mode 100644 index fb2fb603c4..0000000000 --- a/packages/scipion-fluo/.github/workflows/devpi.yaml +++ /dev/null @@ -1,32 +0,0 @@ -name: Publish on Tag - -on: - push: - tags: - - '*' - -jobs: - publish: - runs-on: ubuntu-latest - - steps: - - name: Checkout code - uses: actions/checkout@v4 - - - name: Set up Python - uses: actions/setup-python@v4 - with: - python-version: '3.10' # Replace with your desired Python version - - - name: Install dependencies - run: | - pip install devpi-client # Install devpi-client - - - name: Authenticate and upload to devpi - run: | - devpi use https://pypi.spfluo.ovh - devpi login jean --password=${{ secrets.DEVPI_PASSWORD }} - devpi use jean/dev - devpi upload - env: - DEVPI_PASSWORD: ${{ secrets.DEVPI_PASSWORD }} diff --git a/packages/scipion-fluo/hatch.toml b/packages/scipion-fluo/hatch.toml index eaf15294b8..bdd64d87cb 100644 --- a/packages/scipion-fluo/hatch.toml +++ b/packages/scipion-fluo/hatch.toml @@ -2,6 +2,7 @@ metadata.allow-direct-references = true [version] source = "vcs" +raw-options = { root = "../.." } [build.targets.wheel] packages = ["pwfluo"] diff --git a/packages/scipion-fluo/pyproject.toml b/packages/scipion-fluo/pyproject.toml index ff126dd540..66d63a9d7a 100644 --- a/packages/scipion-fluo/pyproject.toml +++ b/packages/scipion-fluo/pyproject.toml @@ -7,7 +7,7 @@ build-backend = "hatchling.build" [project] name = "scipion-fluo" -version = "0.0.1" +dynamic = ["version"] requires-python = ">=3.8" description = "Base pyworkflow plugin for Fluorescence image processing" readme = "README.rst" @@ -35,4 +35,4 @@ scipion-fluo = "pwfluo.__main__:main" pwfluo = "pwfluo" [tool.uv.sources] -scipion-pyworkflow = {workspace = true} \ No newline at end of file +scipion-pyworkflow = {path = "../scipion-pyworkflow"} \ No newline at end of file diff --git a/packages/scipion-pyworkflow/.github/workflows/devpi.yaml b/packages/scipion-pyworkflow/.github/workflows/devpi.yaml deleted file mode 100644 index 8592419596..0000000000 --- a/packages/scipion-pyworkflow/.github/workflows/devpi.yaml +++ /dev/null @@ -1,32 +0,0 @@ -name: Publish on Tag - -on: - push: - tags: - - '*' - -jobs: - publish: - runs-on: ubuntu-latest - - steps: - - name: Checkout code - uses: actions/checkout@v4 - - - name: Set up Python - uses: actions/setup-python@v4 - with: - python-version: '3.10' # Replace with your desired Python version - - - name: Install dependencies - run: | - pip install devpi-client # Install devpi-client - - - name: Authenticate and upload to devpi - run: | - devpi use https://pypi.spfluo.ovh - devpi login jean --password=${{ secrets.DEVPI_PASSWORD }} - devpi use jean/dev - devpi upload - env: - DEVPI_PASSWORD: ${{ secrets.DEVPI_PASSWORD }} \ No newline at end of file diff --git a/packages/spfluo/.github/workflows/devpi.yaml b/packages/spfluo/.github/workflows/devpi.yaml deleted file mode 100644 index d07d6242f4..0000000000 --- a/packages/spfluo/.github/workflows/devpi.yaml +++ /dev/null @@ -1,32 +0,0 @@ -name: Publish on Tag - -on: - push: - tags: - - '*' - -jobs: - publish: - runs-on: ubuntu-latest - - steps: - - name: Checkout code - uses: actions/checkout@v4 - - - name: Set up Python - uses: actions/setup-python@v4 - with: - python-version: '3.10' # Replace with your desired Python version - - - name: Install dependencies - run: | - pip install devpi-client # Install devpi-client - - - name: Authenticate and upload to devpi - run: | - devpi use http://pypi.spfluo.ovh - devpi login jean --password=${{ secrets.DEVPI_PASSWORD }} - devpi use jean/dev - devpi upload - env: - DEVPI_PASSWORD: ${{ secrets.DEVPI_PASSWORD }} \ No newline at end of file diff --git a/packages/spfluo/hatch.toml b/packages/spfluo/hatch.toml index fdc3e192c6..20fd025ba1 100644 --- a/packages/spfluo/hatch.toml +++ b/packages/spfluo/hatch.toml @@ -1,5 +1,6 @@ [version] source = "vcs" +raw-options = { root = "../.." } [build.targets.wheel] packages = ["spfluo"] diff --git a/packages/spfluo/pyproject.toml b/packages/spfluo/pyproject.toml index cf0f65b6a1..d2b276d914 100644 --- a/packages/spfluo/pyproject.toml +++ b/packages/spfluo/pyproject.toml @@ -18,7 +18,7 @@ dependencies = [ "typing-extensions ; python_version < '3.10'", "ome_types", ] -version = "0.0.1" +dynamic = ["version"] authors = [ { name="Jean Plumail", email="jplumail@unistra.fr" }, ] @@ -32,9 +32,6 @@ classifiers = [ ] [project.optional-dependencies] -gpu = [ - "torch", -] dev = [ "pytest", "pytest-mock", @@ -51,7 +48,7 @@ ab-initio-reconstruction = [ "SimpleITK", ] picking = [ - "spfluo[gpu]", + "torch", "tensorboard", "albumentations", ] @@ -76,4 +73,4 @@ markers = [ ] [tool.uv.sources] -napari-bbox = {workspace = true} \ No newline at end of file +napari-bbox = {path = "../napari-bbox"} \ No newline at end of file diff --git a/pyproject.toml b/pyproject.toml index c20640b332..38dc43da7f 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -20,9 +20,6 @@ Repository = "https://github.com/jplumail/spfluo-app.git" [project.gui-scripts] spfluo-app = "spfluo_app:main" -[project.optional-dependencies] -gpu = ["spfluo[gpu]"] - [tool.hatch.version] source = "vcs" @@ -33,9 +30,6 @@ packages = ["src/spfluo_app"] index-url = "https://pypi.spfluo.ovh/jean/dev/+simple" [tool.uv.sources] -scipion-fluo-singleparticle = { workspace = true } -scipion-app = { workspace = true } -spfluo = { workspace = true } - -[tool.uv.workspace] -members = ["packages/*"] \ No newline at end of file +scipion-fluo-singleparticle = { path = "packages/scipion-fluo-singleparticle" } +scipion-app = { path = "packages/scipion-app" } +spfluo = { path = "packages/spfluo" } \ No newline at end of file diff --git a/uv.lock b/uv.lock deleted file mode 100644 index 6dc76992b2..0000000000 --- a/uv.lock +++ /dev/null @@ -1,3667 +0,0 @@ -version = 1 -requires-python = ">=3.9" -resolution-markers = [ - 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