Merge pull request #71 from irgolic/cleanup-pjt-dev

.git-blame-ignore-revs

@@ -0,0 +1,4 @@
+# Add commit hashes here for ignored commits
+
+f93a09e0378b55a47faebf5690cb036aab4e99a2
+7f4bd896704515f9ee9516db6c6863506c31be7e

.github/workflows/ci.yml

@@ -0,0 +1,79 @@
+name: CI
+on:
+  push:
+    branches:
+      # FIXME replace this with main after merge to main
+      - pjt-dev
+#      - main
+  pull_request:
+    branches:
+      # FIXME replace this with main after merge to main
+      - pjt-dev
+#      - main
+
+concurrency:
+  group: ${{ github.workflow }}-${{ github.event.pull_request.number || github.ref }}
+  cancel-in-progress: true
+
+jobs:
+  pytest:
+    defaults:
+      run:
+        working-directory: python
+    strategy:
+      matrix:
+        python-version: [ 3.12 ]
+        poetry-version: [ 1.7.1 ]
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v2
+
+      - run: pipx install poetry
+      - uses: actions/setup-python@v4
+        with:
+          python-version: ${{ matrix.python-version }}
+          cache: 'poetry'
+
+      - run: poetry install --with dev
+      - run: echo "$(poetry env info --path)/bin" >> $GITHUB_PATH
+
+      - run: make test
+
+  pyright:
+    defaults:
+      run:
+        working-directory: python
+    strategy:
+      matrix:
+        python-version: [3.12]
+        pyright-version: [1.1.343]
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v2
+
+      - run: pipx install poetry
+      - uses: actions/setup-python@v4
+        with:
+          python-version: ${{ matrix.python-version }}
+          cache: 'poetry'
+
+      - run: poetry install --with dev
+      - run: echo "$(poetry env info --path)/bin" >> $GITHUB_PATH
+
+      - uses: jakebailey/pyright-action@v1
+        with:
+          version: ${{ matrix.pyright-version }}
+
+  ruff:
+    defaults:
+      run:
+        working-directory: python
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v3
+      - uses: chartboost/ruff-action@v1
+        with:
+          args: "check"
+      - uses: chartboost/ruff-action@v1
+        with:
+          args: "format --check"

.gitignore

@@ -24,11 +24,13 @@ python/mdvtools/static/*
 python/mdvtools/template/page.html
 .ipynb_checkpoints
 
-python/requirements.txt
 python/dist/
 docs/jsdocs/build/
 docs/maindocs/_build/
 docs/maindocs/autoapi/
 
 venv/
-data/
+data/
+
+.idea
+xvenv/

README.md

@@ -159,6 +159,24 @@ https://myserver.com/path/to/myapp
 * clone the repository
 * npm install
 
+### Git blame without formatting commits
+
+The `.git-blame-ignore-revs` file is used to ignore commits when running `git blame`. This is useful for ignoring formatting commits when trying to find the original author of a line of code. To use it, run:
+
+```bash
+git config -e
+```
+
+And add the following lines:
+
+```toml
+[blame]
+	ignoreRevsFile = ".git-blame-ignore-revs"
+	markIgnoredLines = true
+```
+
+Mark ignored lines will prepend a `?` to the blame commit hashes for indirectly blamed lines.
+
 ### note - this documentation is somewhat deprecated - [for dev-branch](#dev-branch)
 
 You can run a project in development mode, which allows you do debug the JavaScript code and make changes, which will be reflected in the browser.

package.json

@@ -15,7 +15,8 @@
     "build-docs": "sphinx-build -M html docs/maindocs docs/maindocs/_build",
     "build-docs-nix": "source venv/bin/activate && npm run build-docs",
     "build-jsdocs": "jsdoc -c docs/jsdocs/jsdoc.json",
-    "python-setup": "python -m venv venv && source venv/bin/activate && pip install -e python && npm run build-flask-vite",
+    "poetry-setup": "curl -sSL https://install.python-poetry.org | python3 -",
+    "python-setup": "python -m venv venv && source venv/bin/activate && cd python && poetry install --with dev && npm run build-flask-vite",
     "mdv_desktop": "source venv/bin/activate && python -m mdvtools.mdv_desktop",
     "fix_npm_win": "npm config set script-shell \"cmd\""
   },

python/Makefile

@@ -0,0 +1,13 @@
+test:
+	poetry run pytest
+
+type:
+	poetry run pyright
+
+format:
+	poetry run ruff format .
+
+lint:
+	poetry run ruff check . --fix
+
+all: format lint type test

python/readme.md → python/README.md

@@ -3,6 +3,8 @@
 
 ## Installation
 
+### Make virtual environment
+
 It is recommended, but not essential to create a virtual environment so there are no conflicts with modules in the global python.
 
 To create and activate an environment in linux:-
@@ -16,13 +18,30 @@ python -m venv c:\path\to\myenv
 c:\path\to\myenv\Scripts\activate.bat
 ```
 
-Installing mdv (with -e if for development) will include dependencies:
+### Install poetry
+
+Install poetry if it is not already installed. This can be done with the official installer:
 
 ```
-cd MDV/python
-pip install -e .
+curl -sSL https://install.python-poetry.org | python3 -
 ```
 
+Or with pipx:
+```
+pip install pipx
+pipx install poetry
+```
+
+See the [poetry installation instructions](https://python-poetry.org/docs/#installing-with-pipx) for more details and troubleshooting.
+
+### Install MDV
+
+To install MDV, run:
+
+```
+cd MDV/python
+poetry install --with dev
+```
 
 ## Quick Start
 
@@ -33,9 +52,11 @@ To make an empty project, just create an MDVProject object specifying a path. Da
 
 ```python
 from mdvtools.mdvproject import MDVProject
-p=MDVProject("/path/to/myproject")
+
+p = MDVProject("/path/to/myproject")
 df = pd.read_csv("cells.tsv", sep="\t")
-p.add_datasource("cells", df)  #or p.add_datasource("cells", "cells.tsv")
+p.add_datasource("cells", df)  # or p.add_datasource("cells", "cells.tsv")
+
 ```
 
 Initially an empty default view is created. The easiest way to add content is interactively through the browser. To do this, make the project editable and then serve it:-