Fix issues appearing after deploment of PR #293

.editorconfig

@@ -0,0 +1,12 @@
+root = true
+
+[*]
+charset = utf-8
+end_of_line = lf
+insert_final_newline = true
+trim_trailing_whitespace = true
+indent_size = 4
+indent_style = space
+
+[*.{md,yml,yaml,cff}]
+indent_size = 2

.git-blame-ignore-revs

@@ -4,4 +4,7 @@ aa673cb40c34a2481d6f864c6d67ffac9a2b6a16
 
 # 231212, Autoformatting using ruff with expanded rule set //AKe
 fe13c30f4a7f588a29556af37a3545b5662eb4f2
-6899e33d965291455c36c8eff83ed5cc68cd478f
+6899e33d965291455c36c8eff83ed5cc68cd478f
+
+# 240104, Autoformatting using Prettier //AKe
+e22265e0cacd51c3239a790e3c2c9acf7c34be4a

.github/pr_labels.yml

@@ -1,4 +1,4 @@
-version: '1'
+version: "1"
 invalidStatus: "pending"
 labelRule:
   values:

.github/workflows/lint-code.yml

@@ -1,5 +1,11 @@
 name: lint-code
-on: [push]
+on: [push, pull_request]
+
+# Cancel if a newer run is started
+concurrency:
+  group: ${{ github.workflow }}-${{ github.event.pull_request.number || github.ref }}
+  cancel-in-progress: true
+
 jobs:
   # Use ruff to check for code style violations
   ruff-check:
@@ -56,3 +62,74 @@ jobs:
       - name: mypy --> Static type checking
         # Configured in pyprojet.toml
         run: mypy **/*.py
+
+  # Use pipreqs to check for missing dependencies
+  pipreqs-check:
+    runs-on: ubuntu-latest
+    steps:
+      - name: Checkout repository
+        uses: actions/checkout@v4
+      - name: Set up Python
+        uses: actions/setup-python@v4
+        with:
+          python-version: "3.10"
+
+      - name: Install pipreqs
+        run: pip install pipreqs
+
+      - name: Install requirements
+        run: pip install -r requirements.txt
+
+      - name: Run pipreqs
+        run: pipreqs --savepath pipreqs.txt
+
+      - name: Compare requirements
+        run: |
+          # Extract and sort package names
+          awk '{print $1}' $1 | sort -u > "$1".compare
+          awk -F'==' '{print $1}' $2 | sort -u > "$2".compare
+
+          # Compare package lists
+          if cmp -s "$1".compare "$2".compare
+          then
+            echo "Requirements are the same"
+            exit 0
+          else
+            echo "Requirements are different"
+            exit 1
+          fi
+
+    # Use Prettier to check various file formats
+  prettier:
+    runs-on: ubuntu-latest
+    steps:
+      - name: Checkout repository
+        uses: actions/checkout@v4
+      - name: Setup node
+        uses: actions/setup-node@v4
+        with:
+          node-version: "20"
+
+      - name: Install Prettier
+        run: npm install -g prettier
+
+      - name: Run Prettier --check
+        run: prettier --check .
+
+  # Use editorconfig to check all remaining file formats
+  editorconfig:
+    runs-on: ubuntu-latest
+    steps:
+      - name: Checkout repo
+        uses: actions/checkout@v4
+
+      - name: Setup node
+        uses: actions/setup-node@v4
+        with:
+          node-version: "20"
+
+      - name: Install editorconfig-checker
+        run: npm install -g editorconfig-checker
+
+      - name: editorconfig --> Lint files
+        run: editorconfig-checker $(git ls-files | grep -v '.py\|.md\|.json\|.yml\|.yaml\|.html')

.gitignore

@@ -6,4 +6,4 @@ build/
 .ipynb_checkpoints/
 .*_cache/
 *.swp
-__pycache__
+__pycache__

.pre-commit-config.yaml

@@ -1,18 +1,27 @@
 # .pre-commit-config.yaml
 repos:
--   repo: https://github.com/astral-sh/ruff-pre-commit
+  - repo: https://github.com/astral-sh/ruff-pre-commit
     rev: v0.1.6
     hooks:
-    -   id: ruff
-    -   id: ruff-format
--   repo: https://github.com/pre-commit/mirrors-mypy
-    rev: 'v1.7.1'
+      - id: ruff
+      - id: ruff-format
+  - repo: https://github.com/pre-commit/mirrors-mypy
+    rev: "v1.7.1"
     hooks:
-    -   id: mypy
-        additional_dependencies: [
+      - id: mypy
+        additional_dependencies:
+          [
             types-Markdown,
             types-PyYAML,
             types-requests,
             types-setuptools,
             types-tabulate,
-        ]
+          ]
+  - repo: https://github.com/pre-commit/mirrors-prettier
+    rev: "3.0.3"
+    hooks:
+      - id: prettier
+  - repo: https://github.com/editorconfig-checker/editorconfig-checker.python
+    rev: "2.7.2"
+    hooks:
+      - id: editorconfig-checker

README.md

@@ -1,8 +1,10 @@
 # scilifelab_epps
+
 Collection of EPPs for the Scilifelab Stockholm node.
 
 Table of contents
-- [scilifelab\_epps](#scilifelab_epps)
+
+- [scilifelab_epps](#scilifelab_epps)
   - [Overview](#overview)
   - [Installation](#installation)
   - [Development](#development)
@@ -12,41 +14,78 @@ Table of contents
       - [VS Code automation](#vs-code-automation)
     - [Git blame suppression](#git-blame-suppression)
 
-
 ## Overview
+
 The repo is installed inside a designated conda environment on a server hosting Illumina Clarity LIMS.
 
 After installation, the scripts in `scripts/` are addded to the `bin` of the Conda environment, from which they can be called by LIMS.
 
 ## Installation
+
 Inside the repo, run `pip install .`
 
 ## Development
 
 Run `pip install requirements-dev.txt` to install packages used for development and `pip install -e .` to make the installation editable.
 
 ### Automated linting
+
 This repo is configured for automated linting. Linter parameters are defined in `pyproject.toml`.
 
 As of now, we use:
+
 - [ruff](https://docs.astral.sh/ruff/) to perform automated formatting and a variety of lint checks.
+  - Run with `ruff check .` and `ruff format .`
 - [mypy](https://mypy.readthedocs.io/en/stable/) for static type checking and to prevent contradictory type annotation.
+  - Run with `mypy **/*.py`
+- [pipreqs](https://github.com/bndr/pipreqs) to check that the requirement files are up-to-date with the code.
+
+  - This is run with a custom Bash script in GitHub Actions which will only compare the list of package names.
+
+    ```
+    # Extract and sort package names
+    awk '{print $1}' $1 | sort -u > "$1".compare
+    awk -F'==' '{print $1}' $2 | sort -u > "$2".compare
+
+    # Compare package lists
+    if cmp -s "$1".compare "$2".compare
+    then
+      echo "Requirements are the same"
+      exit 0
+    else
+      echo "Requirements are different"
+      exit 1
+    fi
+    ```
+
+- [prettier](https://prettier.io/) to format common languages.
+  - Run with `prettier .`
+- [editorconfig-checker](https://github.com/editorconfig-checker/editorconfig-checker) to enforce `.editorconfig` rules for all files not covered by the tools above.
+  - Run with
+    ```
+    editorconfig-checker $(git ls-files | grep -v '.py\|.md\|.json\|.yml\|.yaml\|.html')
+    ```
 
 #### [GitHub Actions](https://docs.github.com/en/actions)
-Configured in `.github/workflows/lint-code.yml`. Will test all pushed commits, but not change code or prevent merges.
+
+Configured in `.github/workflows/lint-code.yml`. Will test all commits in pushes or pull requests, but not change code or prevent merges.
 
 #### [Pre-commit](https://pre-commit.com/)
+
 Will prevent local commits that fail linting checks. Configured in `.pre-commit-config.yml`.
 
 To set up pre-commit checking:
-1) Run `pip install pre-commit`
-2) Navigate to the repo root
-3) Run `pre-commit install`
+
+1. Run `pip install pre-commit`
+2. Navigate to the repo root
+3. Run `pre-commit install`
 
 This can be disabled with `pre-commit uninstall`
 
 #### VS Code automation
+
 To enable automated linting in VS Code, go the the user `settings.json` and include the following lines:
+
 ```
 "[python]": {
     "editor.defaultFormatter": "charliermarsh.ruff",
@@ -56,13 +95,15 @@ To enable automated linting in VS Code, go the the user `settings.json` and incl
 This will run the `ruff`-mediated linting with the same parameters as the `GitHub Actions` and `pre-commit` every time VS Code is used to format the code in the repository.
 
 To run formatting on save, include the lines:
+
 ```
 "[python]": {
     "editor.formatOnSave": true,
 }
 ```
 
 ### Git blame suppression
+
 When a non-invasive tool is used to tidy up a lot of code, it is useful to supress the Git blame for that particular commit, so the original author can still be traced.
 
-To do this, add the hash of the commit containing the changes to `.git-blame-ignore-revs`, headed by an explanatory comment.
+To do this, add the hash of the commit containing the changes to `.git-blame-ignore-revs`, headed by an explanatory comment.

data/QC_criteria.json

@@ -184,7 +184,7 @@
         }
     },
     "Finished library (by user)": {
-        "MiSeq":{
+        "MiSeq": {
             "default": {
                 "default": {
                     "Concentration": 2,
@@ -208,7 +208,7 @@
                     "Concentration": 2,
                     "Volume (ul)": 110
                 },
-                "XP clustering":{
+                "XP clustering": {
                     "Concentration": 1.5,
                     "Volume (ul)": 25
                 }
@@ -218,7 +218,7 @@
                     "Concentration": 2,
                     "Volume (ul)": 160
                 },
-                "XP clustering":{
+                "XP clustering": {
                     "Concentration": 1.5,
                     "Volume (ul)": 30
                 }
@@ -228,7 +228,7 @@
                     "Concentration": 2,
                     "Volume (ul)": 320
                 },
-                "XP clustering":{
+                "XP clustering": {
                     "Concentration": 1.5,
                     "Volume (ul)": 35
                 }

requirements-dev.txt

@@ -1,8 +1,9 @@
-ruff
 mypy
+pipreqs
 pre-commit
+ruff
 types-PyYAML
 types-requests
 types-tabulate
 types-Markdown
-types-setuptools
+types-setuptools

requirements.txt

@@ -1,6 +1,17 @@
+CouchDB
+flowcell_parser @ git+https://github.com/SciLifeLab/flowcell_parser
 genologics
-couchdb
-markdown
-tabulate
+google_api_python_client
+httplib2
+interop
+Markdown
 numpy
-pandas
+oauth2client
+pandas
+protobuf
+psycopg2
+PyYAML
+Requests
+scilifelab_parsers @ git+https://github.com/SciLifeLab/scilifelab_parsers
+setuptools
+tabulate