Merging dev onto release

.github/workflows/bump-version-dev.yml

@@ -7,53 +7,28 @@ on:
 
 jobs:
   build:
-    if: (! contains(github.event.head_commit.message, '[no bump]'))
 
     name: Bump version
     runs-on: ubuntu-latest
 
     steps:
-    - uses: actions/checkout@v3
+    - uses: actions/checkout@v5
 
     - name: Set up Python
-      uses: actions/setup-python@v4
+      uses: actions/setup-python@v6
       with:
-        python-version: '3.9'
-
-    - name: Set env variables
-      run: |
-        # The next line is very important, otherwise the line after triggers
-        # git to track the permission change, which breaks bump2version API (needs clean git folder)
-        git config core.filemode false
-        chmod +x .github/workflows/utils.sh
-        echo "VERSION_FILE=openpnm/__version__.py" >> $GITHUB_ENV
-        echo "SETUP_CFG_FILE=setup.cfg" >> $GITHUB_ENV
-        echo "${{ github.event.head_commit.message }}"
+        python-version: '3.12'
 
     - name: Install dependencies
       run: |
-        pip install bump2version
+        pip install bump-my-version==1.2.4
+        git config --local user.email "[email protected]"
+        git config --local user.name "GitHub Action"
 
     - name: Bump version (build)
+      shell: bash
       run: |
-        source .github/workflows/utils.sh
-        bump_version build $VERSION_FILE
-        # Note that we don't want to create a new tag for "builds"
-
-    # - name: Commit files
-    #   run: |
-    #     REPOSITORY=${INPUT_REPOSITORY:-$GITHUB_REPOSITORY}
-    #     remote_repo="https://${GITHUB_ACTOR}:${{ secrets.PUSH_ACTION_TOKEN }}@github.com/${REPOSITORY}.git"
-
-    #     git config --local user.email "[email protected]"
-    #     git config --local user.name "GitHub Action"
-
-    #     # Commit version bump to dev ([no ci] to avoid infinite loop)
-    #     git commit -m "Bump version number (build) [no ci]" -a
-    #     git push "${remote_repo}" dev
-
-    - name: Commit files
-      uses: stefanzweifel/git-auto-commit-action@v4
-      with:
-        commit_message: Bump version number (build part)
-        commit_author: Author <[email protected]>
+        bump-my-version bump pre_n --commit --message "Bump version number on dev"
+        git push origin HEAD:dev
+        git push --tags
+

.github/workflows/bump-version-release.yml

@@ -0,0 +1,60 @@
+name: Bump Version (release)
+
+on:
+  push:
+    branches:
+      - release
+
+jobs:
+  build:
+
+    name: Bump version
+    runs-on: ubuntu-latest
+
+    steps:
+    - uses: actions/checkout@v5
+
+    - name: Set up Python
+      uses: actions/setup-python@v6
+      with:
+        python-version: '3.12'
+
+    - name: Install dependencies
+      run: |
+        pip install bump-my-version==1.2.4
+        git config --local user.email "[email protected]"
+        git config --local user.name "GitHub Action"
+
+    - name: Bump version (patch)
+      if: contains(github.event.head_commit.message, '#patch')
+      run: |
+        bump-my-version bump patch --commit --message "Bump version number on release"
+        git push origin HEAD:release
+        git push --tags
+
+    - name: Bump version (minor)
+      if: contains(github.event.head_commit.message, '#minor')
+      run: |
+        bump-my-version bump minor --commit --message "Bump version number on release"
+        git push origin HEAD:release
+        git push --tags
+
+    - name: Bump version (major)
+      if: contains(github.event.head_commit.message, '#major')
+      run: |
+        bump-my-version bump major --commit --message "Bump version number on release"
+        git push origin HEAD:release
+        git push --tags
+
+    - name: Create Pull Request to merge back release into dev
+      uses: repo-sync/pull-request@v2
+      with:
+        source_branch: "release"                          # If blank, default: triggered branch
+        destination_branch: "dev"                         # If blank, default: master
+        pr_title: "Merge release branch back into dev"
+        pr_body: "Changes made to the release branch (if any), plus the version bump."
+        pr_assignee: "jgostick"                           # Comma-separated list (no spaces)
+        pr_label: "high priority"                         # Comma-separated list (no spaces)
+        pr_draft: false                                   # Creates pull request as draft
+        pr_allow_empty: true                              # Creates pull request even if there are no changes
+        github_token: ${{ secrets.GITHUB_TOKEN }}

pyproject.toml

@@ -1,6 +1,6 @@
 [project]
 name = "openpnm"
-dynamic = ["version"]
+version = "3.5.5-dev3"
 description = "A framework for conducting pore network modeling simulations of multiphase transport in porous materials"
 authors = [{ name = "OpenPNM Team", email = "[email protected]" }]
 maintainers = [
@@ -95,8 +95,35 @@ dev = [
 requires = ["setuptools>=80"]
 build-backend = "setuptools.build_meta"
 
-[tool.setuptools]
-packages = ["openpnm"]
+[tool.bumpversion]
+current_version = "3.5.5-dev3"
+parse = """(?x)
+    (?P<major>0|[1-9]\\d*)\\.
+    (?P<minor>0|[1-9]\\d*)\\.
+    (?P<patch>0|[1-9]\\d*)
+    (?:
+        -                             # dash separator for pre-release section
+        (?P<pre_l>[a-zA-Z-]+)         # pre-release label
+        (?P<pre_n>0|[1-9]\\d*)        # pre-release version number
+    )?                                # pre-release section is optional
+"""
+serialize = [
+    "{major}.{minor}.{patch}-{pre_l}{pre_n}",
+    "{major}.{minor}.{patch}",
+]
+search = "{current_version}"
+replace = "{new_version}"
+regex = false
+ignore_missing_version = false
+tag = true
+sign_tags = false
+tag_name = "v{new_version}"
+tag_message = "Bump version: {current_version} → {new_version}"
+allow_dirty = false
+commit = false
+message = "Bump version: {current_version} → {new_version}"
+commit_args = ""
 
-[tool.setuptools.dynamic]
-version = {attr = "openpnm.__version__.__version__"}
+[tool.bumpversion.parts.pre_l]
+values = ["dev", "rc", "final"]
+optional_value = "dev"

openpnm/__init__.py → src/openpnm/__init__.py

@@ -9,15 +9,24 @@
 """
 
 import logging
-
+import importlib.metadata as _metadata
+import tomllib as _toml
+import numpy as _np
 from rich.logging import RichHandler
 
+
+# try:
+#     __version__ = _metadata.version(__package__ or __name__)
+# except _metadata.PackageNotFoundError:
+with open("./pyproject.toml", "rb") as f:
+    data = _toml.load(f)
+    __version__ = data["project"]["version"]
+
 FORMAT = "%(message)s"
 logging.basicConfig(
     format=FORMAT, datefmt="[%X]", handlers=[RichHandler(rich_tracebacks=True)]
 )
 
-import numpy as _np
 
 from . import (
     _skgraph,
@@ -37,5 +46,3 @@
 from .utils import Project, Workspace
 
 _np.seterr(divide='ignore', invalid='ignore')
-
-__version__ = utils._get_version()

openpnm/_skgraph/queries/_qupc.py → src/openpnm/_skgraph/queries/_qupc.py

@@ -8,6 +8,8 @@
     'qupc_update',
     'qupc_compress',
     'qupc_reduce',
+    'qupc_union',
+    'qupc_find',
 ]
 
 
@@ -42,6 +44,20 @@ def qupc_reduce(arr):
         arr[i] = arr[arr[i]]
     return arr
 
+@njit
+def qupc_union(arr, ind, val):
+    indp=qupc_find(arr, ind)
+    valp=qupc_find(arr, val)
+    arr[indp]=valp
+    return arr
+
+@njit
+def qupc_find(arr, ind):
+    while arr[ind] != ind:
+        arr[ind] = arr[arr[ind]]
+        ind = arr[ind]
+    return ind
+
 
 if __name__ == '__main__':
     a = qupc_initialize(10)
@@ -60,4 +76,4 @@ def qupc_reduce(arr):
     qupc_reduce(a)
     qupc_compress(a)
     assert np.all(a == [0, 0, 1, 2, 1, 1, 1, 1, 0, 3])
-    print(a)
+    print(a)