Merge pull request #437 from OpenCOMPES/v1_feature_branch

Upgrade to V1

.cspell/custom-dictionary.txt

@@ -38,6 +38,7 @@ caldir
 calib
 calibdict
 caplog
+capsys
 cdeform
 cdeformfield
 cdisp
@@ -77,6 +78,8 @@ datastreams
 datestring
 ddir
 delaxes
+delayeds
+delenv
 Desy
 Deutsches
 dfield
@@ -85,12 +88,14 @@ dfpart
 dfpid
 dictionarized
 dictmerge
+DLDAUX
 DOOCS
 dpkg
 dropna
 dset
 dsets
 dtype
+dtypes
 easimon
 ecalibdict
 electronanalyser
@@ -125,6 +130,7 @@ ftype
 fwhm
 genindex
 getgid
+getgrgid
 getmtime
 gpfs
 griddata
@@ -290,6 +296,7 @@ ptargs
 pullrequest
 pval
 pyarrow
+pydantic
 pydata
 pyenv
 pygments
@@ -330,6 +337,7 @@ scipy
 SDIAG
 sdir
 segs
+setp
 sfile
 shutil
 Sixten
@@ -340,6 +348,8 @@ splinewarp
 stackax
 stackaxis
 stepsize
+subchannel
+subchannels
 subdir
 subdirs
 subfolders
@@ -401,6 +411,8 @@ xpos
 xratio
 xrng
 xscale
+xticklabels
+xticks
 xtrans
 Xuser
 xval
@@ -411,6 +423,8 @@ ylabel
 ypos
 yratio
 yscale
+yticklabels
+yticks
 ytrans
 zain
 Zenodo

.github/workflows/benchmark.yml

@@ -4,9 +4,12 @@ name: benchmark
 on:
     workflow_dispatch:
     push:
-        branches: [ main, create-pull-request/patch ]
-        paths-ignore:
-          pyproject.toml
+      branches: [ main]
+    pull_request:
+      branches: [ main ]
+
+env:
+  UV_SYSTEM_PYTHON: true
 
 jobs:
   benchmark:
@@ -16,28 +19,32 @@ jobs:
       - name: Check out the repository
         uses: actions/checkout@v4
         with:
-          lfs: true
+          fetch-depth: 0
 
       - uses: tibdex/github-app-token@v1
         id: generate-token
         with:
           app_id: ${{ secrets.APP_ID }}
           private_key: ${{ secrets.APP_PRIVATE_KEY }}
 
-      # Use cached python and dependencies, install poetry
-      - name: "Setup Python, Poetry and Dependencies"
-        uses: packetcoders/action-setup-cache-python-poetry@main
+      # Setup python
+      - name: Set up Python 3.10
+        uses: actions/setup-python@v5
         with:
-          python-version: 3.8
-          poetry-version: 1.2.2
+          python-version: "3.10"
+
+      - name: Install dependencies
+        run: |
+          curl -LsSf https://astral.sh/uv/install.sh | sh
 
-      - name: Install project dependencies
-        run: poetry install
+      - name: Install package
+        run: |
+          uv pip install ".[dev]"
 
       # Run benchmarks
-      - name: Run benchmarks on python 3.8
+      - name: Run benchmarks on python 3.10
         run: |
-          poetry run pytest --full-trace --show-capture=no -sv benchmarks/benchmark_*.py
+          pytest --full-trace --show-capture=no -sv benchmarks/benchmark_*.py
 
       - name: Obtain git status
         id: status

.github/workflows/documentation.yml

@@ -5,12 +5,14 @@ on:
     branches: [ main ]
     tags: [ v* ]
     paths:
-      - sed/**/*
+      - src/sed/**/*
       - tutorial/**
       - .github/workflows/documentation.yml
   # Allows you to run this workflow manually from the Actions tab
   workflow_dispatch:
 
+env:
+  UV_SYSTEM_PYTHON: true
 
 jobs:
   build:
@@ -26,69 +28,50 @@ jobs:
           remove-android: 'true'
           remove-docker-images: 'true'
 
-      #  Check out repo and set up Python
-      - name: Check out the repository
-        uses: actions/checkout@v4
+      # Check out repo and set up Python
+      - uses: actions/checkout@v4
         with:
-          lfs: true
+          fetch-depth: 0
 
-      # Use cached python and dependencies, install poetry
-      - name: "Setup Python, Poetry and Dependencies"
-        uses: packetcoders/action-setup-cache-python-poetry@main
+      # Setup python
+      - name: Set up Python 3.10
+        uses: actions/setup-python@v5
         with:
-          python-version: 3.9
-          poetry-version: 1.8.3
+          python-version: "3.10"
+
+      - name: Install dependencies
+        run: |
+          curl -LsSf https://astral.sh/uv/install.sh | sh
 
-      - name: Install notebook dependencies
-        run: poetry install -E notebook --with docs
+      - name: Install package
+        run: |
+          uv pip install ".[docs,notebook]"
 
       - name: Install pandoc
         run: |
           sudo wget https://github.com/jgm/pandoc/releases/download/3.1.8/pandoc-3.1.8-1-amd64.deb
           sudo dpkg -i pandoc-3.1.8-1-amd64.deb
 
-      # rm because hextof_workflow notebook can not run outside maxwell
       - name: copy tutorial files to docs
         run: |
           cp -r $GITHUB_WORKSPACE/tutorial $GITHUB_WORKSPACE/docs/
-          cp -r $GITHUB_WORKSPACE/sed/config $GITHUB_WORKSPACE/docs/sed
-
+          mkdir -p $GITHUB_WORKSPACE/docs/src/sed
+          cp -r $GITHUB_WORKSPACE/src/sed/config $GITHUB_WORKSPACE/docs/src/sed/
 
       - name: download RAW data
         # if: steps.cache-primes.outputs.cache-hit != 'true'
         run: |
           cd $GITHUB_WORKSPACE/docs
-          poetry run python scripts/download_data.py
+          python scripts/download_data.py
 
       - name: build parquet files
         run: |
           cd $GITHUB_WORKSPACE/docs
-          poetry run python scripts/build_flash_parquets.py
-          poetry run python scripts/build_sxp_parquets.py
-
-      # to be removed later. This theme doesn't support <3.9 python and our lock file contains 3.8
-      - name: install pydata-sphinx-theme
-        run: |
-          poetry run pip install pydata-sphinx-theme
-
-      - name: Change version for develop build
-        if: startsWith(github.ref, 'refs/heads/') && github.ref != 'refs/heads/main'
-        run: |
-          VERSION=`sed -n 's/^version = "\(.*\)".*/\1/p' $GITHUB_WORKSPACE/pyproject.toml`
-          MOD_VERSION=$VERSION".dev0"
-          echo $MOD_VERSION
-          sed -i "s/^version = \"$VERSION\"/version = \"$MOD_VERSION\"/" $GITHUB_WORKSPACE/pyproject.toml
-
-      - name: Change version for release build
-        if: startsWith(github.ref, 'refs/tags/')
-        run: |
-          OLD_VERSION=`sed -n 's/^version = "\(.*\)".*/\1/p' $GITHUB_WORKSPACE/pyproject.toml`
-          NEW_VERSION=`echo ${GITHUB_REF#refs/tags/} | sed -n 's/^v\(.*\)/\1/p'`
-          echo $NEW_VERSION
-          sed -i "s/^version = \"$OLD_VERSION\"/version = \"$NEW_VERSION\"/" $GITHUB_WORKSPACE/pyproject.toml
+          python scripts/build_flash_parquets.py
+          python scripts/build_sxp_parquets.py
 
       - name: build Sphinx docs
-        run: poetry run sphinx-build -b html $GITHUB_WORKSPACE/docs $GITHUB_WORKSPACE/_build
+        run: sphinx-build -b html $GITHUB_WORKSPACE/docs $GITHUB_WORKSPACE/_build
 
       - name: Upload artifact
         uses: actions/upload-artifact@v4
@@ -102,17 +85,12 @@ jobs:
     needs: build
     steps:
       - name: Checkout docs repo
-        uses: actions/checkout@v2
+        uses: actions/checkout@v4
         with:
           repository: ${{ github.repository_owner }}/docs
           token: ${{ secrets.GITHUB_TOKEN }}
           path: 'docs-repo'
 
-      - name: Set up Python 3.9
-        uses: actions/setup-python@v4
-        with:
-          python-version: 3.9
-
       - name: Setup SSH
         uses: webfactory/[email protected]
         with:
@@ -129,11 +107,16 @@ jobs:
         run: |
           if [[ $GITHUB_REF == refs/tags/* ]]; then
             VERSION=${GITHUB_REF#refs/tags/}
-            echo "folder=sed/$VERSION" >> $GITHUB_OUTPUT
-            rm docs-repo/sed/stable
-            rm -rf docs-repo/sed/latest
-            ln -s -r docs-repo/sed/$VERSION docs-repo/sed/stable
-            ln -s -r docs-repo/sed/$VERSION docs-repo/sed/latest
+              echo "folder=sed/$VERSION" >> $GITHUB_OUTPUT
+            if [[ $VERSION == *a* ]]; then
+              rm -rf docs-repo/sed/latest
+              ln -s -r docs-repo/sed/$VERSION docs-repo/sed/latest
+            else
+              rm -rf docs-repo/sed/stable
+              rm -rf docs-repo/sed/latest
+              ln -s -r docs-repo/sed/$VERSION docs-repo/sed/stable
+              ln -s -r docs-repo/sed/$VERSION docs-repo/sed/latest
+            fi
           elif [[ $GITHUB_REF == refs/heads/main ]]; then
             rm -rf docs-repo/sed/latest
             echo "folder=sed/latest" >> $GITHUB_OUTPUT

.github/workflows/linting.yml

@@ -3,8 +3,9 @@ name: linting
 # Triggers the workflow on push for all branches
 on:
   push:
-    paths-ignore:
-      pyproject.toml
+
+env:
+  UV_SYSTEM_PYTHON: true
 
 jobs:
   lint:
@@ -13,27 +14,34 @@ jobs:
       # Check out repo and set up Python
       - uses: actions/checkout@v4
         with:
-          lfs: true
+          fetch-depth: 0
 
-      # Use cached python and dependencies, install poetry
-      - name: "Setup Python, Poetry and Dependencies"
-        uses: packetcoders/action-setup-cache-python-poetry@main
+      # Setup python
+      - name: Set up Python 3.10
+        uses: actions/setup-python@v5
         with:
-          python-version: 3.8
-          poetry-version: 1.2.2
+          python-version: "3.10"
+
+      - name: Install dependencies
+        run: |
+          curl -LsSf https://astral.sh/uv/install.sh | sh
+
+      - name: Install package
+        run: |
+          uv pip install ".[dev]"
 
       # Linting steps, execute all linters even if one fails
       - name: ruff
         run:
-          poetry run ruff sed tests
+          ruff src/sed tests
       - name: ruff formatting
         if: ${{ always() }}
         run:
-          poetry run ruff format --check sed tests
+          ruff format --check src/sed tests
       - name: mypy
         if: ${{ always() }}
         run:
-          poetry run mypy sed tests
+          mypy src/sed tests
       - name: spellcheck
         if: ${{ always() }}
         uses: streetsidesoftware/cspell-action@v6