Merge branch '2maz/workflows'

.github/workflows/gh-pages.yml

@@ -0,0 +1,58 @@
+name: Deploy github pages
+
+on:
+  # Runs on pushes targeting the default branch
+  push:
+    branches: ["main"]
+  # Allows you to run this workflow manually from the Actions tab
+  workflow_dispatch:
+
+# Sets permissions of the GITHUB_TOKEN to allow deployment to GitHub Pages
+permissions:
+  contents: read
+  pages: write
+  id-token: write
+
+# Allow only one concurrent deployment, skipping runs queued between the run in-progress and latest queued.
+# However, do NOT cancel in-progress runs as we want to allow these production deployments to complete.
+concurrency:
+  group: "pages"
+  cancel-in-progress: false
+
+jobs:
+  # Single deploy job since we're just deploying
+  deploy:
+    environment:
+      name: github-pages
+      url: ${{ steps.deployment.outputs.page_url }}
+    runs-on: ubuntu-latest
+    steps:
+      - name: Checkout
+        uses: actions/checkout@v4
+
+      - uses: actions/setup-python@v5
+        with:
+          python-version: '3.10'
+
+      - name: Install pip
+        run: python -m pip install -U pip
+
+      - name: Install tox
+        run: python -m pip install tox
+
+      - name: Generate page content
+        run: |
+          tox -e build_docs;
+
+      - name: Setup Pages
+        uses: actions/configure-pages@v4
+
+      - name: Upload artifact
+        uses: actions/upload-pages-artifact@v3
+        with:
+          path: _build/html
+
+      - name: Deploy to GitHub Pages
+        id: deployment
+        uses: actions/deploy-pages@v4
+

.github/workflows/lint.yml

@@ -0,0 +1,36 @@
+name: Lint python package
+
+on:
+  push:
+  pull_request:
+  workflow_dispatch:
+
+jobs:
+  lint:
+    runs-on: ubuntu-latest
+
+    steps:
+    - uses: actions/checkout@v4
+
+    - uses: actions/setup-python@v5
+      with:
+        python-version: "3.10"
+
+    - name: Install pip
+      run: python -m pip install -U pip
+
+    - name: Install tox
+      run: python -m pip install tox
+
+    - name: Run linter
+      run: tox -e lint
+
+    - name: Upload artifact
+      uses: actions/upload-artifact@v4
+      with:
+        name: lint-codeclimate
+        path: artifacts/lint/lint-codeclimate.json
+        retention-days: 3
+        overwrite: true
+
+

.github/workflows/test.yml

@@ -0,0 +1,34 @@
+name: Test python package
+
+on:
+  push:
+    paths:
+      - tests/**
+      - src/**
+  pull_request:
+  workflow_dispatch:
+
+jobs:
+  test:
+    runs-on: ubuntu-latest
+
+    steps:
+      - uses: actions/checkout@v4
+      - uses: actions/setup-python@v5
+        with:
+          python-version: '3.10'
+
+      - name: Install pip
+        run: python -m pip install -U pip
+
+      - name: Install package
+        run: python -m pip install -e .[dev,test]
+
+      - name: Install tox
+        run: python -m pip install tox
+
+      - name: Install os dependencies
+        run: sudo apt install -y graphviz
+
+      - name: Run tests
+        run: tox -e py

CONTRIBUTING.md

@@ -4,7 +4,7 @@ Great see that you are interested in contributing to 'damast'.
 
 To make the process as smooth as possible for all involed parties, you will find some instructions
 below.  In case there is some information missing, or you feel lost, do not
-hesitate to ask or [open an issue](https://gitlab.com/simula-srl/damast/-/issues/new)
+hesitate to ask or [open an issue](https://github.com/simula/damast/issues/new)
  on this project.
 
  ## Installation
@@ -65,7 +65,7 @@ to run a particular test case (-k) and redirecting the output to stdout (-s).
 ## Merge Requests
 
 Please fork the repository and push your code change into a branch.
-Then create a [new merge request](https://gitlab.com/simula-srl/damast/-/merge_requests/new) from this branch.
+Then create a new merge request from this branch.
 
 Generally, read through the documentation first to understand the main ideas and some underlying assumptions of this project.
 If you intend to change some of the behavior, please try to validate by reading the documentation or opening an issue whether

README.md

@@ -1,6 +1,6 @@
 # damast: Creation of reproducible data processing pipelines
 
-Documentation at: https://simula-srl.gitlab.io/damast
+Documentation at: https://simula.github.io/damast
 
 ## Installation and Development Setup
 
@@ -29,7 +29,7 @@ Create your venv and activate it:
 Clone the repo and install:
 
 ```
-    git clone https://gitlab.com/simula-srl/damast
+    git clone https://github.com/simula/damast
     cd damast
     pip install -e ".[test,dev]"
 

pyproject.toml

@@ -56,6 +56,7 @@ repository = "https://gitlab.com/simula-srl/damast"
 
 [project.optional-dependencies]
 dev = [
+    "astroid<3",
     "flake8-gl-codeclimate",
     "isort",
     "jupyter-book",
@@ -66,7 +67,8 @@ dev = [
 test = [
     "coverage",
     "pytest",
-    "pytest-cov"
+    "pytest-cov",
+    "pydot"
 ]
 
 [project.scripts]

src/damast/__init__.py

@@ -1,3 +1,5 @@
+"""Main module"""
+
 from damast import cli, core, data_handling, domains
 from damast.core import artifacts, describe, input, output
 

src/damast/data_handling/exploration.py

@@ -35,8 +35,14 @@ def plot_lat_lon(*,
     :return: Path to the file
     """
 
-    plt.scatter(x=df[longitude_name].evaluate(),
-                y=df[latitude_name].evaluate(),
+    longitude = df[longitude_name].evaluate()
+    latitude = df[latitude_name].evaluate()
+
+    # .copy() to address ValueError: assignment destination is read-only
+    # raised in numpy/ma/core.py:3528: in mask
+    #      self.__setmask__(value)
+    plt.scatter(x=longitude.copy(),
+                y=latitude.copy(),
                 alpha=1)
     plt.xlim(-180, 180)
     plt.ylim(-90, 90)