[WIP] Abstract XRF spectrum

.bumpversion.cfg

@@ -5,13 +5,13 @@ tag = True
 tag_name = {new_version}
 current_version = 0.0.0
 parse = (?P<major>\d+)\.(?P<minor>\d+)\.(?P<patch>\d+)(\.(?P<release>[a-z]+)(?P<dev>\d+))?
-serialize = 
+serialize =
 	{major}.{minor}.{patch}.{release}{dev}
 	{major}.{minor}.{patch}
 
 [bumpversion:part:release]
 optional_value = gamma
-values = 
+values =
 	dev
 	rc
 	gamma

.editorconfig

@@ -0,0 +1,12 @@
+# EditorConfig is awesome: https://EditorConfig.org
+
+# top-most EditorConfig file
+root = true
+
+[*]
+indent_style = space
+indent_size = 4
+end_of_line = lf
+charset = utf-8
+trim_trailing_whitespace = true
+insert_final_newline = false

.github/workflows/coverage_report.yml

@@ -22,7 +22,7 @@ jobs:
         sudo apt-get update && sudo apt-get install -y libsasl2-dev libldap2-dev libssl-dev
         python -m pip install --upgrade pip
         python -m pip install poetry --user
-        python -m poetry install
+        python -m poetry install --extras=tango
 
     - name: Run and write pytest
       run: |

.github/workflows/pages.yaml

@@ -0,0 +1,79 @@
+---
+
+
+name: "Pages"
+
+concurrency:
+  group: "pages"
+
+on:
+  push:
+  pull_request:
+
+jobs:
+
+  "pages-build":
+
+    runs-on: "ubuntu-22.04"
+
+    steps:
+
+      - name: "Checkout"
+        uses: "actions/checkout@v4"  # tested with v4.1.0
+
+      - name: "Set up Python 3.8"
+        uses: "actions/setup-python@v4"  # tested with v4.7.0
+        with:
+          python-version: "3.8"
+
+      - name: "Install OpenLDAP's dev package with apt"
+        run: |
+          sudo apt-get update
+          sudo apt-get install --no-install-recommends --yes libldap2-dev libsasl2-dev
+
+      - name: "Install dependencies with Poetry"
+        run: |
+          python -m pip install --upgrade pip
+          python -m pip install poetry --user
+          python -m poetry install --only=docs,main
+
+      - name: "Build documentation with Sphinx"
+        run: |
+          poetry run make --directory=./docs/ html
+
+      - name: "Upload artifact for GitHub Pages"
+        # This could potentially be run only when we intend to deploy...
+        # ...but it can be useful to have the artifact for debugging
+        # if: "github.ref_name == github.event.repository.default_branch"
+        uses: "actions/upload-pages-artifact@v2"  # tested with v2.0.0
+        with:
+          path: "docs/build/html"
+
+  "pages-deploy":
+
+    if: "github.ref_name == github.event.repository.default_branch"
+
+    environment:
+      name: "github-pages"
+      url: "${{ steps.deployment.outputs.page_url }}"
+
+    needs:
+      - "pages-build"
+
+    permissions:
+      pages: "write"
+      id-token: "write"
+
+    runs-on: "ubuntu-22.04"
+
+    steps:
+
+      - name: "Setup GitHub Pages"
+        uses: "actions/configure-pages@v3"  # tested with v3.0.6
+
+      - name: "Deploy to GitHub Pages"
+        id: "deployment"
+        uses: "actions/deploy-pages@v2"  # tested with 2.0.4
+
+
+...  # EOF

.github/workflows/pre-commit.yml

@@ -8,10 +8,10 @@ jobs:
     steps:
     - uses: actions/checkout@v3
 
-    - name: Set up Python 3.7
+    - name: Set up Python 3.8
       uses: actions/setup-python@v4
       with:
-        python-version: "3.7"
+        python-version: "3.8"
 
     - name: Install openldap
       run: |
@@ -26,5 +26,4 @@ jobs:
 
     - name: Run Pre-Commit
       run: |
-        # Disable linting for now
-        # poetry run pre-commit run --all-files
+        poetry run pre-commit run --all-files

.github/workflows/tests.yml

@@ -25,12 +25,7 @@ jobs:
         run: |
           python -m pip install --upgrade pip
           python -m pip install poetry --user
-          python -m poetry install
-
-      - name: Linting and code quality checks
-        run: |
-          # Disabled for now
-          # python -m poetry run pre-commit run --all-files
+          python -m poetry install --extras=tango
 
       - name: Test with pytest
         run: |

.gitignore

@@ -3,7 +3,36 @@
 *~
 *swp
 *swo
+.venv/
+__pycache__/
+*.py[cod]
+.Python
+env/
+build/
+develop-eggs/
+downloads/
+eggs/
+.eggs/
+lib/
+lib64/
+parts/
+sdist/
+dist/
+var/
+*.egg-info/
+.installed.cfg
+*.egg
+
+# Unit test / coverage reports
+htmlcov/
+.tox/
 .coverage
+.coverage.*
+.cache
+nosetests.xml
+coverage.xml
+*,cover
+*.log
 
-.venv/
+.DS_Store
 .vscode/

.pre-commit-config.yaml

@@ -1,19 +1,16 @@
 default_language_version:
-  python: python3.7
+  python: python3.8
 repos:
   - repo: https://github.com/python-poetry/poetry
     rev: 1.5.0
     hooks:
       - id: poetry-check
-        language_version: python3.7
-      - id: poetry-lock
-        language_version: python3.7
+#      - id: poetry-lock
   - repo: https://github.com/myint/autoflake
     rev: v1.6.0
     hooks:
       - id: autoflake
         name: Autoflake
-        exclude: (utils/pyispyb_client/|deprecated/|mxcubecore/HardwareObjects/(ALBA|ASLS|DESY|EMBL|ESRF|LNLS|MAXIV|SOLEIL|ANSTO|Gphl|Arinax))
         args:
           - --expand-star-imports
           - --ignore-init-module-imports
@@ -25,14 +22,42 @@ repos:
     hooks:
     - id: black
       name: Black
-      language_version: python3.7
-      exclude: (utils/pyispyb_client/|deprecated/|mxcubecore/HardwareObjects/(ALBA|ASLS|DESY|EMBL|ESRF|LNLS|MAXIV|SOLEIL|ANSTO|Gphl|Arinax))
   - repo: https://github.com/pre-commit/pre-commit-hooks
     rev: v4.3.0
     hooks:
-      # - id: trailing-whitespace
-      # - id: end-of-file-fixer
-      #   exclude: (deprecated/|mxcubecore/HardwareObjects/(ALBA|ASLS|DESY|EMBL|ESRF|LNLS|MAXIV|SOLEIL|ANSTO|Gphl|Arinax))
+      - id: trailing-whitespace
+        #
+        # Exclude files below from trailing-whitespace checks until we get around fixing them.
+        # This way we can check that all other files are trailing-whitespace clean in CI.
+        #
+        exclude: |
+            (?x)^(
+                mxcubecore/configuration/.*|
+                mxcubecore/HardwareObjects/(MotorsNPosition|PlateManipulator|TangoMotor)\.py|
+                mxcubecore/HardwareObjects/(PlateManipulatorMaintenance|TangoLimaMpegVideo)\.py|
+                mxcubecore/HardwareObjects/DESY/P11(EDNACharacterisation|BackLight|Shutter|Collect|DetectorCover)\.py|
+                mxcubecore/HardwareObjects/LNLS/LNLS(PilatusDet|Energy|Diffractometer)\.py|
+                mxcubecore/HardwareObjects/LNLS/EPICS(Actuator|Motor|NState)\.py|
+                mxcubecore/HardwareObjects/LNLS/set_transmission_mnc.py|
+                mxcubecore/HardwareObjects/EMBL/EMBL(Energy|DoorInterlock|OnlineProcessing)\.py|
+                mxcubecore/HardwareObjects/mockup/(ISPyBClient|Motor|PlateManipulator)Mockup\.py|
+                mxcubecore/HardwareObjects/abstract/(AbstractXRFSpectrum|sample_changer/Crims)\.py|
+                mxcubecore/HardwareObjects/Gphl/Transcal2MiniKappa\.py|
+                mxcubecore/HardwareObjects/SOLEIL/PX2/PX2Resolution\.py|
+                mxcubecore/HardwareObjects/ESRF/ID29XRFSpectrum\.py
+            )$
+      - id: end-of-file-fixer
+        #
+        # Exclude files below from end-of-file-fixer checks until we get around fixing them.
+        # This way we can check that all other files are end-of-file-fixer clean in CI.
+        #
+        exclude: |
+            (?x)^(
+                mxcubecore/configuration/.*|
+                mxcubecore/HardwareObjects/mockup/(Shutter|Motor)Mockup\.py|
+                mxcubecore/HardwareObjects/LNLS/EPICS(NState|Motor)\.py|
+                mxcubecore/HardwareObjects/EMBL/EMBLOnlineProcessing\.py
+            )$
       - id: check-case-conflict
       - id: check-merge-conflict
         # exclude files where underlines are not distinguishable from merge conflicts

.readthedocs.yaml

@@ -0,0 +1,28 @@
+---
+
+
+# .readthedocs.yaml
+# Read the Docs configuration file
+# See https://docs.readthedocs.io/en/stable/config-file/v2.html for details
+
+
+# This uses custom commands, because we need to install dependencies
+# from both Conda and Poetry.
+
+
+version: 2
+
+build:
+
+  os: "ubuntu-22.04"
+
+  tools:
+    python: "mambaforge-22.9"
+
+  commands:
+    - "mamba env create --file conda-environment-dev.yml --force"
+    - "mamba run --name mxcubecore poetry install --only=docs,main"
+    - "mamba run --name mxcubecore sphinx-build -T -E -b html -c ./docs/ ./docs/source/ ${READTHEDOCS_OUTPUT}/html/"
+
+
+...  # EOF