Merge pull request #288 from bessagroup/pr/2.0.0

Pull request from pr/2.0.0 to main
bessagroup · Jan 24, 2025 · b6f7d3a · b6f7d3a
2 parents 8b8b744 + 2bbb042
commit b6f7d3a
Show file tree

Hide file tree

Showing 155 changed files with 14,980 additions and 9,945 deletions.
diff --git a/.coveragerc b/.coveragerc
@@ -5,6 +5,7 @@ source = src
 omit =
     tests/*
     **/__init__.py
+    src/f3dasm/_src/experimentdata/_newdata.py
 
 [report]
 # Regexes for lines to exclude from consideration

diff --git a/.github/workflows/pr_to_main.yml b/.github/workflows/pr_to_main.yml
@@ -56,7 +56,10 @@ jobs:
           python -m pip install --upgrade pip
           pip install -r requirements_dev.txt
       - name: Build documentation
-        run: |
+        uses: r-lib/actions/setup-pandoc@v2
+        with:
+          pandoc-version: '3.1.2' # The pandoc version to download (if necessary) and use.
+      - run: |
           sphinx-build -b html ./docs/source ./docs/build/html
   build-package:
     strategy:

diff --git a/.github/workflows/pr_to_pr.yml b/.github/workflows/pr_to_pr.yml
@@ -67,7 +67,10 @@ jobs:
         run: |
           pip install -r requirements_dev.txt
       - name: Build documentation
-        run: |
+        uses: r-lib/actions/setup-pandoc@v2
+        with:
+          pandoc-version: '3.1.2' # The pandoc version to download (if necessary) and use.
+      - run: |
           sphinx-build -b html ./docs/source ./docs/build/html
   build-package:
     strategy:

diff --git a/.github/workflows/release.yaml b/.github/workflows/release.yaml
@@ -0,0 +1,134 @@
+name: release
+
+on:
+  push:
+    tags:
+      - "[0-9]+.[0-9]+.[0-9]+"
+      - "[0-9]+.[0-9]+.[0-9]+a[0-9]+"
+      - "[0-9]+.[0-9]+.[0-9]+b[0-9]+"
+      - "[0-9]+.[0-9]+.[0-9]+rc[0-9]+"
+
+env:
+  PACKAGE_NAME: "f3dasm"
+  OWNER: "bessagroup"
+
+jobs:
+  details:
+    runs-on: ubuntu-latest
+    outputs:
+      new_version: ${{ steps.release.outputs.new_version }}
+      suffix: ${{ steps.release.outputs.suffix }}
+      tag_name: ${{ steps.release.outputs.tag_name }}
+    steps:
+      - uses: actions/checkout@v2
+
+      - name: Extract tag and Details
+        id: release
+        run: |
+          if [ "${{ github.ref_type }}" = "tag" ]; then
+            TAG_NAME=${GITHUB_REF#refs/tags/}
+            NEW_VERSION=$(echo $TAG_NAME | awk -F'-' '{print $1}')
+            SUFFIX=$(echo $TAG_NAME | grep -oP '[a-z]+[0-9]+' || echo "")
+            echo "new_version=$NEW_VERSION" >> "$GITHUB_OUTPUT"
+            echo "suffix=$SUFFIX" >> "$GITHUB_OUTPUT"
+            echo "tag_name=$TAG_NAME" >> "$GITHUB_OUTPUT"
+            echo "Version is $NEW_VERSION"
+            echo "Suffix is $SUFFIX"
+            echo "Tag name is $TAG_NAME"
+          else
+            echo "No tag found"
+            exit 1
+          fi
+
+  check_pypi:
+    needs: details
+    runs-on: ubuntu-latest
+    steps:
+      - name: Fetch information from PyPI
+        run: |
+          response=$(curl -s https://pypi.org/pypi/${{ env.PACKAGE_NAME }}/json || echo "{}")
+          latest_previous_version=$(echo $response | awk '/"releases":/ {flag=1} flag' | grep -oP '"\d+\.\d+(\.\d+)*"' | tr -d '"' | sort -rV | head -n 1)
+          if [ -z "$latest_previous_version" ]; then
+            echo "Package not found on PyPI."
+            latest_previous_version="0.0.0"
+          fi
+          echo "Latest version on PyPI: $latest_previous_version"
+          echo "latest_previous_version=$latest_previous_version" >> $GITHUB_ENV
+
+      - name: Compare versions and exit if not newer
+        run: |
+          NEW_VERSION=${{ needs.details.outputs.new_version }}
+          LATEST_VERSION=$latest_previous_version
+          if [ "$(printf '%s\n' "$LATEST_VERSION" "$NEW_VERSION" | sort -rV | head -n 1)" != "$NEW_VERSION" ] || [ "$NEW_VERSION" == "$LATEST_VERSION" ]; then
+            echo "The new version $NEW_VERSION is not greater than the latest version $LATEST_VERSION on PyPI."
+            exit 1
+          else
+            echo "The new version $NEW_VERSION is greater than the latest version $LATEST_VERSION on PyPI."
+          fi
+
+  setup_and_build:
+    needs: [details, check_pypi]
+    runs-on: ubuntu-latest
+    steps:
+      - name: Checkout
+        uses: actions/checkout@v2
+
+      - name: Set up Python
+        uses: actions/setup-python@v4
+        with:
+          python-version: "3.8"
+
+      - name: Install build dependencies
+        run: python -m pip install -U setuptools wheel build
+
+      - name: Build the package
+        run: python -m build .
+
+      - name: Upload artifacts
+        uses: actions/upload-artifact@v3
+        with:
+          name: dist
+          path: dist/
+
+  pypi_publish:
+    name: Upload release to PyPI
+    needs: [setup_and_build, details]
+    runs-on: ubuntu-latest
+    environment:
+      name: release
+    permissions:
+      id-token: write
+    steps:
+      - name: Download artifacts
+        uses: actions/download-artifact@v3
+        with:
+          name: dist
+          path: dist/
+
+      - name: Publish distribution to PyPI
+        uses: pypa/gh-action-pypi-publish@release/v1
+
+  github_release:
+    name: Create GitHub Release
+    needs: [setup_and_build, details]
+    runs-on: ubuntu-latest
+    permissions:
+      contents: write
+    steps:
+      - name: Checkout Code
+        uses: actions/checkout@v3
+        with:
+          fetch-depth: 0
+
+      - name: Download artifacts
+        uses: actions/download-artifact@v3
+        with:
+          name: dist
+          path: dist/
+
+      - name: Create GitHub Release
+        id: create_release
+        env:
+          GH_TOKEN: ${{ github.token }}
+        run: |
+          gh release create ${{ needs.details.outputs.tag_name }} dist/* --title ${{ needs.details.outputs.tag_name }} --generate-notes
diff --git a/README.md b/README.md
@@ -54,7 +54,7 @@ or
 
 ```bash
 # PyPI
-$ conda install f3dasm
+$ conda install conda-forge::f3dasm
 ```
 
 * Follow the complete [installation instructions](https://f3dasm.readthedocs.io/en/latest/rst_doc_files/general/installation.html) to get going!
@@ -100,7 +100,7 @@ If you find any **issues, bugs or problems** with this template, please use the
 
 ## License
 
-Copyright 2024, Martin van der Schelling
+Copyright 2025, Martin van der Schelling
 
 All rights reserved.
 

diff --git a/VERSION b/VERSION
@@ -1 +1 @@
-1.5.4
+2.0.0
diff --git a/docs/requirements.txt b/docs/requirements.txt
@@ -1,6 +1,7 @@
 sphinx
-sphinx_rtd_theme
+sphinx-book-theme
 sphinxcontrib-bibtex
 sphinx_autodoc_typehints
 sphinx-tabs==3.4.4
-sphinx-gallery
+nbsphinx
+ipykernel
diff --git a/docs/source/conf.py b/docs/source/conf.py
@@ -7,8 +7,6 @@
 import os
 import sys
 
-from sphinx_gallery.sorting import FileNameSortKey
-
 # -- Search path for extensions and modules -----------------------------------
 # If extensions or Python modules are in a different directory than this file,
 # then add these directories to sys.path so that Sphinx can search for them
@@ -26,9 +24,9 @@
 
 project = 'f3dasm'
 author = 'Martin van der Schelling'
-copyright = '2024, Martin van der Schelling'
-version = '1.5.4'
-release = '1.5.4'
+copyright = '2025, Martin van der Schelling'
+version = '2.0.0'
+release = '2.0.0'
 
 
 # -- General configuration ----------------------------------------------------
@@ -38,26 +36,25 @@
 # coming with Sphinx (named 'sphinx.ext.*') or your custom ones.
 
 extensions = ['sphinx.ext.duration',
-              'sphinx_rtd_theme',
               'sphinx.ext.autodoc',
               'sphinx.ext.napoleon',
               'sphinx.ext.autosummary',
               'sphinx.ext.intersphinx',
               'sphinx.ext.viewcode',
               'sphinx_autodoc_typehints',
               'sphinx_tabs.tabs',
-              'sphinx_gallery.gen_gallery',]
-
-sphinx_gallery_conf = {
-    'examples_dirs': ['../../examples'],   # path to your example scripts
-    'gallery_dirs': ['auto_examples'],
-    'reference_url': {'sphinx_gallery': None, },
-    'backreferences_dir': 'gen_modules/backreferences',
-    'doc_module': ('f3dasm',),
-    "filename_pattern": r"/*\.py",
-    "within_subsection_order": FileNameSortKey,
-    "nested_sections": False,
-}
+              'nbsphinx',]
+
+# sphinx_gallery_conf = {
+#     'examples_dirs': ['../../examples'],   # path to your example scripts
+#     'gallery_dirs': ['auto_examples'],
+#     'reference_url': {'sphinx_gallery': None, },
+#     'backreferences_dir': 'gen_modules/backreferences',
+#     'doc_module': ('f3dasm',),
+#     "filename_pattern": r"/*\.py",
+#     "within_subsection_order": FileNameSortKey,
+#     "nested_sections": False,
+# }
 
 # Source: https://www.sphinx-doc.org/en/master/usage/configuration.html#confval-source_suffix
 source_suffix = {'.rst': 'restructuredtext', }
@@ -122,15 +119,17 @@
 # Source: https://www.sphinx-doc.org/en/master/usage/configuration.html#confval-html_theme_path
 on_rtd = os.environ.get('READTHEDOCS', None) == 'True'
 if on_rtd:
-    import sphinx_rtd_theme
-    html_theme = 'sphinx_rtd_theme'
-    html_theme_path = [sphinx_rtd_theme.get_html_theme_path()]
+    # import sphinx_rtd_theme
+    # html_theme = 'sphinx_rtd_theme'
+    # html_theme_path = [sphinx_rtd_theme.get_html_theme_path()]
+    html_theme = 'sphinx_book_theme'
 else:
     # Source: https://sphinx-rtd-theme.readthedocs.io/en/stable/index.html
     # Requires installation of Python package 'sphinx_rtd_theme'
-    import sphinx_rtd_theme
-    html_theme = 'sphinx_rtd_theme'
-    html_theme_path = [sphinx_rtd_theme.get_html_theme_path()]
+    # import sphinx_rtd_theme
+    # html_theme = 'sphinx_rtd_theme'
+    # html_theme_path = [sphinx_rtd_theme.get_html_theme_path()]
+    html_theme = 'sphinx_book_theme'
 
 # Source: https://www.sphinx-doc.org/en/master/usage/configuration.html#confval-html_static_path
 html_static_path = ['_static', ]

diff --git a/docs/source/index.rst b/docs/source/index.rst
@@ -9,7 +9,7 @@ f3dasm
 
 .. toctree::
    :name: gettingstartedtoc
-   :caption: Getting started
+   :caption: 🚶 Getting started
    :maxdepth: 3
    :hidden:
    :includehidden:
@@ -20,21 +20,21 @@ f3dasm
 
 .. toctree::
    :name: functionalitiestoc
-   :caption: Functionalities
+   :caption: 🌊 Functionalities
    :maxdepth: 3
    :hidden:
    :includehidden:
 
-   auto_examples/index
+   rst_doc_files/gallery
    rst_doc_files/defaults
 
 .. toctree::
    :name: apitoc
-   :caption: API
+   :caption: 📖 Reference
    :hidden:
 
    rst_doc_files/reference/index.rst
-   API reference <_autosummary/f3dasm>
+   API documentation <_autosummary/f3dasm>
 
 .. toctree::
    :name: licensetoc

diff --git a/docs/source/license.rst b/docs/source/license.rst
@@ -3,7 +3,7 @@
 BSD 3-Clause License
 ====================
 
-Copyright (c) 2022, Martin van der Schelling
+Copyright (c) 2025, Martin van der Schelling
 
 All rights reserved.