liesel-gam 0.0.5.dev0__tar.gz → 0.1.0a3__tar.gz

liesel_gam-0.0.5.dev0/.github/workflows/pytest-notebooks.yml → liesel_gam-0.1.0a3/.github/workflows/doctest.yml

@@ -1,8 +1,15 @@
-name: notebooks
+name: doctest
 
 on:
   push:
     branches: [main]
+  pull_request:
+    branches: [main, develop]
+  workflow_dispatch: # trigger manually from GitHub UI
+
+concurrency:
+  group: ${{ github.workflow }}-${{ github.ref }}
+  cancel-in-progress: true
 
 jobs:
   pytest:
@@ -31,12 +38,16 @@ jobs:
           r-version: 'release'
           use-public-rspm: true
 
-      - name: Install Package
-        run: uv sync --locked --group dev
+      - name: Fix R library path
+        run: |
+          echo "LD_LIBRARY_PATH=$(R RHOME)/lib:$LD_LIBRARY_PATH" >> $GITHUB_ENV
 
-      - name: Add R shared libraries to LD_LIBRARY_PATH
+      - name: Install R dependencies
         run: |
-          echo "LD_LIBRARY_PATH=$(python -m rpy2.situation LD_LIBRARY_PATH):\$LD_LIBRARY_PATH" >> $GITHUB_ENV
+          Rscript -e "install.packages('arrow')"
+
+      - name: Install Package
+        run: uv sync --locked --group dev
 
       - name: Debug R environment
         run: |
@@ -47,4 +58,4 @@ jobs:
 
 
       - name: Run pytest
-        run: uv run pytest tests/notebooks --nbval-lax --nbval-current-env
+        run: uv run pytest --doctest-modules src/liesel_gam

{liesel_gam-0.0.5.dev0 → liesel_gam-0.1.0a3}/.github/workflows/pre-commit.yml

@@ -4,7 +4,12 @@ on:
   push:
     branches: [main]
   pull_request:
-    branches: [main]
+    branches: [main, develop]
+  workflow_dispatch: # trigger manually from GitHub UI
+
+concurrency:
+  group: ${{ github.workflow }}-${{ github.ref }}
+  cancel-in-progress: true
 
 jobs:
   pre-commit:

{liesel_gam-0.0.5.dev0 → liesel_gam-0.1.0a3}/.github/workflows/pypi.yml

@@ -36,7 +36,7 @@ jobs:
         run: uv build
 
       - name: Publish package
-        uses: pypa/gh-action-pypi-publish@v1.5.0
+        uses: pypa/gh-action-pypi-publish@v1.13.0
         with:
           user: __token__
           password: ${{ secrets.PYPI_UPLOAD }}

liesel_gam-0.1.0a3/.github/workflows/pytest-notebooks.yml

@@ -0,0 +1,62 @@
+name: notebooks
+
+on:
+  push:
+    branches: [main]
+  pull_request:
+    branches: [main, develop]
+  workflow_dispatch: # trigger manually from GitHub UI
+
+concurrency:
+  group: ${{ github.workflow }}-${{ github.ref }}
+  cancel-in-progress: true
+
+jobs:
+  pytest:
+    runs-on: ubuntu-latest
+    timeout-minutes: 15
+
+    strategy:
+      matrix:
+        python-version: ["3.13"]
+        notebook-dir: ["composite", "lin", "multivariate", "univariate"]
+
+    steps:
+      - name: Check out repository
+        uses: actions/checkout@v4
+
+      - name: Install uv and set the python version
+        uses: astral-sh/setup-uv@v5
+        with:
+          python-version: ${{ matrix.python-version }}
+          enable-cache: true
+          cache-dependency-glob: "uv.lock"
+
+
+      - name: Set up R
+        uses: r-lib/actions/setup-r@v2
+        with:
+          r-version: 'release'
+          use-public-rspm: true
+
+      - name: Fix R library path
+        run: |
+          echo "LD_LIBRARY_PATH=$(R RHOME)/lib:$LD_LIBRARY_PATH" >> $GITHUB_ENV
+
+      - name: Install R dependencies
+        run: |
+          Rscript -e "install.packages(c('arrow', 'svglite'))"
+
+      - name: Install Package
+        run: uv sync --locked --group dev
+
+      - name: Debug R environment
+        run: |
+          echo "R_HOME=$(R RHOME)"
+          echo "LD_LIBRARY_PATH=$LD_LIBRARY_PATH"
+          find $(R RHOME) -name methods.so
+          find $(R RHOME) -name libR.so
+
+
+      - name: Run pytest
+        run: uv run pytest notebooks/${{ matrix.notebook-dir }} --nbval-lax --nbval-current-env

liesel_gam-0.1.0a3/.github/workflows/pytest-pull.yml

@@ -0,0 +1,59 @@
+name: pytest-pull
+
+on:
+  pull_request:
+    branches: [main, develop]
+  workflow_dispatch: # trigger manually from GitHub UI
+
+concurrency:
+  group: ${{ github.workflow }}-${{ github.ref }}
+  cancel-in-progress: true
+
+jobs:
+  pytest:
+    runs-on: ubuntu-latest
+    timeout-minutes: 10
+
+    strategy:
+      matrix:
+        python-version: ["3.13"]
+
+    steps:
+      - name: Check out repository
+        uses: actions/checkout@v4
+
+      - name: Install uv and set the python version
+        uses: astral-sh/setup-uv@v5
+        with:
+          python-version: ${{ matrix.python-version }}
+          enable-cache: true
+          cache-dependency-glob: "uv.lock"
+
+
+      - name: Set up R
+        uses: r-lib/actions/setup-r@v2
+        with:
+          r-version: 'release'
+          use-public-rspm: true
+
+      - name: Fix R library path
+        run: |
+          echo "LD_LIBRARY_PATH=$(R RHOME)/lib:$LD_LIBRARY_PATH" >> $GITHUB_ENV
+
+      - name: Install R dependencies
+        run: |
+          Rscript -e "install.packages('arrow')"
+
+      - name: Install Package
+        run: uv sync --locked --group dev
+
+      - name: Debug R environment
+        run: |
+          echo "R_HOME=$(R RHOME)"
+          echo "LD_LIBRARY_PATH=$LD_LIBRARY_PATH"
+          find $(R RHOME) -name methods.so
+          find $(R RHOME) -name libR.so
+
+
+      - name: Run pytest
+        run: uv run pytest --cov=liesel_gam

{liesel_gam-0.0.5.dev0 → liesel_gam-0.1.0a3}/.github/workflows/pytest.yml

@@ -3,6 +3,11 @@ name: pytest
 on:
   push:
     branches: [main]
+  workflow_dispatch: # trigger manually from GitHub UI
+
+concurrency:
+  group: ${{ github.workflow }}-${{ github.ref }}
+  cancel-in-progress: true
 
 jobs:
   pytest:
@@ -31,12 +36,16 @@ jobs:
           r-version: 'release'
           use-public-rspm: true
 
-      - name: Install Package
-        run: uv sync --locked --group dev
+      - name: Fix R library path
+        run: |
+          echo "LD_LIBRARY_PATH=$(R RHOME)/lib:$LD_LIBRARY_PATH" >> $GITHUB_ENV
 
-      - name: Add R shared libraries to LD_LIBRARY_PATH
+      - name: Install R dependencies
         run: |
-          echo "LD_LIBRARY_PATH=$(python -m rpy2.situation LD_LIBRARY_PATH):\$LD_LIBRARY_PATH" >> $GITHUB_ENV
+          Rscript -e "install.packages('arrow')"
+
+      - name: Install Package
+        run: uv sync --locked --group dev
 
       - name: Debug R environment
         run: |

{liesel_gam-0.0.5.dev0 → liesel_gam-0.1.0a3}/.gitignore

@@ -176,3 +176,12 @@ cython_debug/
 /.vscode
 /tests/data
 .DS_Store
+notebooks/test_ti_smooth.ipynb
+notebooks/test_mrf.R
+img/Präsentation1.pptx
+covtest.sh
+/docs/source/generated
+notebooks/multivariate/test_tx_optim.ipynb
+/doctests
+notebooks/univariate/test_ps_nosmooth.ipynb
+notebooks/univariate/test_ps_smooth_constant_prior.ipynb

liesel_gam-0.1.0a3/.readthedocs.yaml

@@ -0,0 +1,27 @@
+# Read the Docs configuration file
+# See https://docs.readthedocs.io/en/stable/config-file/v2.html for details
+
+# Required
+version: 2
+
+# Set the OS, Python version, and other tools you might need
+build:
+  os: ubuntu-24.04
+  tools:
+    python: "3.13"
+  jobs:
+    install:
+      - python -m pip install --upgrade pip
+      - python -m pip install . --group dev
+      - python -m pip list
+
+# Build documentation in the "docs/" directory with Sphinx
+sphinx:
+   configuration: docs/source/conf.py
+
+# Optionally, but recommended,
+# declare the Python requirements required to build your documentation
+# See https://docs.readthedocs.io/en/stable/guides/reproducible-builds.html
+# python:
+#    install:
+#    - requirements: docs/requirements.txt