diff comparison from last pull request

.dvc/.gitignore

@@ -0,0 +1,3 @@
+/config.local
+/tmp
+/cache

.dvc/config

@@ -0,0 +1,5 @@
+[core]
+    remote = calkit
+['remote "calkit"']
+    url = https://api.calkit.io/projects/symbiotic-engineering/openflash/dvc
+    auth = custom

.dvcignore

@@ -0,0 +1,3 @@
+# Add patterns of files dvc should ignore, which could improve
+# the performance. Learn more at
+# https://dvc.org/doc/user-guide/dvcignore

.github/workflows/deploy-docs.yml

@@ -0,0 +1,84 @@
+name: Deploy Sphinx Docs to GitHub Pages
+
+on:
+  workflow_dispatch: # gets dispatched from PR tagging workflow or manually
+
+concurrency:
+  group: "pages"
+  cancel-in-progress: true
+
+jobs:
+  build-and-deploy:
+    runs-on: ubuntu-latest
+
+    permissions:
+      pages: write
+      id-token: write
+
+    environment:
+      name: github-pages
+      url: ${{ steps.deployment.outputs.page_url }}
+
+    steps:
+      - name: Checkout repository
+        uses: actions/checkout@v4
+        with:
+          fetch-depth: 0
+
+      - name: Set up Python
+        uses: actions/setup-python@v5
+        with:
+          python-version: "3.10"
+
+      - name: Install pandoc (system-level)
+        run: |
+          sudo apt-get update
+          sudo apt-get install -y pandoc
+
+      - name: Install Python dependencies and local package
+        run: |
+          python -m pip install --upgrade pip
+          pip install -r requirements.txt 
+          pip install .
+
+      - name: Build Sphinx documentation
+        run: |
+          sphinx-build -b html docs/ docs/_build/html
+
+      - name: Copy Streamlit app to docs output root
+        run: |
+          cp docs/_static/app_streamlit.html docs/_build/html/
+
+      # Add _headers for Stlite Cross-Origin Isolation ---
+      - name: Add Cross-Origin Headers for Stlite
+        run: |
+          echo "/*" > docs/_build/html/_headers
+          echo "  Cross-Origin-Opener-Policy: same-origin" >> docs/_build/html/_headers
+          echo "  Cross-Origin-Embedder-Policy: require-corp" >> docs/_build/html/_headers
+
+      # Create ZIP Artifact for Download
+      - name: Compress Docs to ZIP
+        run: zip -r docs-preview.zip docs/_build/html
+
+      - name: Upload Docs Preview Artifact
+        uses: actions/upload-artifact@v4
+        with:
+          name: docs-preview
+          path: docs-preview.zip # Uploads the newly created .zip file
+          retention-days: 1
+
+      - name: Upload artifact # This is the Pages artifact uploader
+        uses: actions/upload-pages-artifact@v3
+        with:
+          path: docs/_build/html
+
+      - name: Get latest tag to decide whether to deploy
+        run: |
+          echo "tag=$(git describe --tags --abbrev=0)"
+          echo "tag=$(git describe --tags --abbrev=0)" >> $GITHUB_OUTPUT
+        id: get-tag
+
+      - name: Deploy to GitHub Pages
+        id: deployment
+        if: ${{ !contains(steps.get-tag.outputs.tag , 'rc') }}
+        uses: actions/deploy-pages@v4

.github/workflows/draft-pdf.yml

@@ -0,0 +1,30 @@
+name: Draft PDF
+on:
+  push:
+    paths:
+      - 'pubs/joss/paper.md'
+      - 'pubs/joss/paper.bib'
+      - 'pubs/figs/**'  # To trigger on image changes
+      - '.github/workflows/draft-pdf.yml' # To trigger on workflow changes
+
+jobs:
+  paper:
+    runs-on: ubuntu-latest
+    name: Paper Draft
+    steps:
+      - name: Checkout
+        uses: actions/checkout@v4
+      - name: Build draft PDF
+        uses: openjournals/openjournals-draft-action@master
+        with:
+          journal: joss
+          # This should be the path to the paper within your repo.
+          paper-path: pubs/joss/paper.md
+      - name: Upload
+        uses: actions/upload-artifact@v4
+        with:
+          name: paper
+          # This is the output path where Pandoc will write the compiled
+          # PDF. Note, this should be the same directory as the input
+          # paper.md
+          path: pubs/joss/paper.pdf

.github/workflows/pr-tagging.yml

@@ -0,0 +1,97 @@
+name: PR Tagging and RC Tag Management
+
+# This workflow creates a tag for pull requests into the main branch.
+# The tag for open pull requests is of the form vX.Y.ZrcPRNUM
+# where X.Y.Z is the base version (which is incremented according to the PR title)
+# and PRNUM is the pull request number (to prevent conflicts for multiple PRs open at once).
+# By default the Z number is incremented, but if the PR title contains [major] or [minor],
+# the X or Y version numbers are incremented respectively.
+# The tag for merged pull requests is of the form vX.Y.Z with no additions.
+
+on:
+  pull_request:
+    types: [opened, reopened, synchronize, closed]
+    branches:
+      - main
+  workflow_dispatch:
+
+permissions:
+  contents: write
+  issues: write
+  actions: write
+  packages: write
+  id-token: write
+
+jobs:
+  manage-pr-tags:
+    runs-on: ubuntu-latest
+    steps:
+      - name: Checkout
+        uses: actions/checkout@v4
+        with:
+          fetch-depth: 0
+
+      - name: Compute base version (bump patch/minor/major from PR title)
+        id: compute_base
+        run: |
+          PR_TITLE="${{ github.event.pull_request.title || '' }}"
+          base=$(bash scripts/compute_base.sh "$PR_TITLE")
+          echo "base=$base" >> $GITHUB_OUTPUT
+
+      - name: Check if rc tag already exists and if so compute rc-dev tag
+        id: check_rc
+        run: |
+          rc_tag="${{ steps.compute_base.outputs.base }}rc${{ github.event.pull_request.number }}"
+          if git rev-parse "$rc_tag" >/dev/null 2>&1; then
+            devN=$(git rev-list --count $rc_tag..HEAD)
+            rc_dev_tag="${rc_tag}dev${devN}"
+          else
+            rc_dev_tag="${rc_tag}"
+          fi
+          echo "rc_dev_tag=${rc_dev_tag}" >> $GITHUB_OUTPUT
+
+      - name: Create rc tag
+        id: create_rc
+        if: ${{ github.event.action == 'opened' || github.event.action == 'reopened' || github.event.action == 'synchronize' }}
+        uses: rickstaa/action-create-tag@v1
+        with:
+          tag:  "${{ steps.check_rc.outputs.rc_dev_tag }}"
+          message: "Release ${{ steps.check_rc.outputs.rc_dev_tag }}"
+          commit_sha: ${{ github.event.pull_request.head.sha }}
+
+      - name: Create final tag
+        if: ${{ github.event.action == 'closed' && github.event.pull_request.merged == true }}
+        uses: rickstaa/action-create-tag@v1
+        with:
+          tag: ${{ steps.compute_base.outputs.base }}
+          message: "Release ${{ steps.compute_base.outputs.base }}"
+          commit_sha: ${{ github.event.pull_request.merge_commit_sha }}
+
+      - name: Dispatch docs deploy and publish package workflows
+        if: ${{ github.event.action == 'closed' && github.event.pull_request.merged == false }} == false
+        uses: actions/github-script@v7
+        with:
+          github-token: ${{ secrets.GITHUB_TOKEN }}
+          script: |
+            try {
+              const owner = context.repo.owner;
+              const repo = context.repo.repo;
+              const workflow_id_1 = 'deploy-docs.yml';
+              const workflow_id_2 = 'publish-package.yml';
+
+              let ref;
+              if (${{ github.event.action == 'closed' && github.event.pull_request.merged == true }}) {
+                ref = '${{ github.ref_name }}';
+              }
+              else { 
+                ref = '${{ github.head_ref  || github.ref }}';
+              }
+
+              const resp  = await github.rest.actions.createWorkflowDispatch({ owner, repo, workflow_id: workflow_id_1, ref });
+              const resp2 = await github.rest.actions.createWorkflowDispatch({ owner, repo, workflow_id: workflow_id_2, ref });
+              console.log('docs dispatch response', resp && resp.status ? resp.status : resp);
+              console.log('package dispatch response', resp2 && resp2.status ? resp2.status : resp2);
+            } catch (err) {
+              console.error('dispatch failed', err && err.status ? { status: err.status, message: err.message } : err);
+              throw err;
+            }

.github/workflows/publish-package.yml

@@ -0,0 +1,109 @@
+name: Build and Publish on Tag
+
+# This workflow builds and publishes the package to PyPI and Anaconda
+# when a tag is pushed. If the tag is a release candidate (contains 'rc'),
+# it is published to TestPyPI and the Anaconda package is not uploaded.
+
+on:
+  push:
+    tags:
+      - 'v*.*.*'
+  workflow_dispatch: # gets dispatched from PR tagging workflow or manually
+  workflow_call:
+
+permissions:
+  contents: write
+  packages: write
+  id-token: write
+
+jobs:
+  determine-tag:
+    runs-on: ubuntu-latest
+    outputs:
+      publish: ${{ steps.decide.outputs.publish }}
+      tag:     ${{ steps.get-tag.outputs.tag }}
+    steps:
+      - name: Checkout
+        uses: actions/checkout@v4
+        with:
+          fetch-depth: 0
+      - name: Get latest tag to decide whether to publish
+        id: get-tag
+        run: |
+          echo "tag=$(git describe --tags --abbrev=0)"
+          echo "tag=$(git describe --tags --abbrev=0)" >> $GITHUB_OUTPUT
+      - name: Decide whether to publish
+        id: decide
+        run: |
+          echo "publish=${{ !contains(steps.get-tag.outputs.tag, 'rc') }}" >> $GITHUB_OUTPUT
+
+  build-and-publish:
+    runs-on: ubuntu-latest
+    needs: determine-tag
+    environment:
+      name: ${{ needs.determine-tag.outputs.publish == 'true' && 'pypi' || 'testpypi' }}
+      # the fact that the environment name uses an output is the reason this workflow is split into two jobs
+      url: https://pypi.org/project/open-flash/
+    steps:
+      - name: Checkout
+        uses: actions/checkout@v4
+        with:
+          fetch-depth: 0
+
+      - name: Set up Python
+        uses: actions/setup-python@v5
+        with:
+          python-version: '3.11'
+
+      - name: Install build tools
+        run: pip install build twine
+
+      - name: Build distribution packages
+        run: python -m build
+
+      - name: Publish package to PyPI
+        uses: pypa/gh-action-pypi-publish@release/v1
+        with:
+          repository-url:  ${{ needs.determine-tag.outputs.publish == 'true' && 'https://upload.pypi.org/legacy/' || 'https://test.pypi.org/legacy/' }}
+          verbose: true
+
+      - name: Setup Miniconda
+        uses: conda-incubator/setup-miniconda@v3
+        with:
+          python-version: 3.11
+          environment-file: conda-recipe/build_env.yaml
+          auto-update-conda: false
+          auto-activate-base: false
+          show-channel-urls: true
+
+      - name: Build and upload conda packages
+        uses: uibcdf/action-build-and-upload-conda-packages@2a98398b2f382f5ead0feebda695a13474e107f8
+        id: conda-build-and-upload
+        with:
+          meta_yaml_dir: conda-recipe 
+          label: main
+          user: sea-lab
+          token: ${{ secrets.ANACONDA_TOKEN }}
+          upload: ${{ needs.determine-tag.outputs.publish }}
+
+      - name: Re-format output paths
+        id: reformat-paths
+        # Needed to have the correct newline-separated files format for the following release step
+        run: |
+          paths=$(tr ' ' '\n' <<< "${{steps.conda-build-and-upload.outputs.paths}}")
+          echo "newline-separated-paths=$paths" >> $GITHUB_OUTPUT
+
+      - name: Check validity of citation.cff
+        uses: citation-file-format/cffconvert-github-action@2.0.0
+        if: always()
+        with:
+          args: "-i ./CITATION.cff -f zenodo --validate --show-trace"
+
+      - name: Create GitHub release
+        if: ${{ needs.determine-tag.outputs.publish == 'true' }}
+        uses: softprops/action-gh-release@v2
+        with:
+          tag_name: ${{ needs.determine-tag.outputs.tag }}
+          generate_release_notes: true
+          fail_on_unmatched_files: true
+          files: ${{steps.reformat-paths.outputs.newline-separated-paths}}

.gitignore

@@ -127,6 +127,7 @@ venv/
 ENV/
 env.bak/
 venv.bak/
+.new_env
 
 # Spyder project settings
 .spyderproject
@@ -204,4 +205,5 @@ html/
 # mat data files
 *.mat
 
-.vscode/settings.json
+# vscode configuration files
+.vscode/