add basic ci pipeline for mdmix3

.devcontainer/devcontainer.json

@@ -0,0 +1,55 @@
+// For format details, see https://aka.ms/devcontainer.json. For config options, see the
+// README at: https://github.com/devcontainers/templates/tree/main/src/docker-existing-dockerfile
+{
+	"name": "Existing Dockerfile",
+	"build": {
+		// Sets the run context to one level up instead of the .devcontainer folder.
+		"context": "..",
+		// Update the 'dockerFile' property if you aren't using the standard 'Dockerfile' filename.
+		"dockerfile": "../Dockerfile",
+		"target": "development"
+	},
+	"customizations": {
+		"vscode": {
+			"settings": {
+				"python.languageServer": "Pylance",
+				"python.testing.pytestEnabled": true,
+				"python.testing.pytestArgs": [
+					"tests"
+				],
+				"[python]": {
+					"editor.formatOnSave": true,
+					"editor.codeActionsOnSave": {
+						"source.organizeImports": true
+					},
+					"editor.defaultFormatter": "charliermarsh.ruff"
+				},
+				"files.autoSave": "afterDelay",
+				"files.autoSaveDelay": 1000
+			},
+			"extensions": [
+				"ms-python.python",
+				"littlefoxteam.vscode-python-test-adapter",
+				"ms-vsliveshare.vsliveshare",
+				"mhutchie.git-graph",
+				"ms-toolsai.jupyter",
+				"charliermarsh.ruff"
+			]
+		}
+	}
+
+	// Features to add to the dev container. More info: https://containers.dev/features.
+	// "features": {},
+
+	// Use 'forwardPorts' to make a list of ports inside the container available locally.
+	// "forwardPorts": [],
+
+	// Uncomment the next line to run commands after the container is created.
+	// "postCreateCommand": "cat /etc/os-release",
+
+	// Configure tool-specific properties.
+	// "customizations": {},
+
+	// Uncomment to connect as an existing user other than the container default. More info: https://aka.ms/dev-containers-non-root.
+	// "remoteUser": "devcontainer"
+}

.github/workflows/ci.yaml

@@ -0,0 +1,68 @@
+name: Lint and Test
+
+on:
+  workflow_dispatch:
+  push:
+    branches: [ "mdmix3-dev" ]
+
+  pull_request:
+    branches: [ "mdmix3-dev" ]
+
+jobs:
+  build-dev:
+    runs-on: ubuntu-latest
+    permissions:
+      contents: read
+      packages: write
+    outputs:
+      REPOSITORY: ${{ steps.repository_lower.outputs.REPOSITORY }}
+    steps:
+      - name: Checkout repository
+        uses: actions/checkout@v4
+
+      - name: Setup Docker buildx
+        uses: docker/setup-buildx-action@v3
+
+      - name: Log into registry ghcr.io
+        uses: docker/login-action@v3
+        with:
+          registry: ghcr.io
+          username: ${{ github.actor }}
+          password: ${{ secrets.GITHUB_TOKEN }}
+
+      - name: set repository lower case
+        id: repository_lower
+        run: |
+          echo REPOSITORY=$(echo ${{ github.repository }} | tr '[:upper:]' '[:lower:]') >> $GITHUB_OUTPUT
+
+      - name: Build and push Docker image
+        uses: docker/build-push-action@v6
+        with:
+          context: .
+          tags: ghcr.io/${{ steps.repository_lower.outputs.REPOSITORY }}_dev
+          push: true
+          target: development
+          cache-from: type=gha
+          cache-to: type=gha,mode=max
+
+  test:
+    needs: build-dev
+    runs-on: ubuntu-latest
+    container:
+      image: ghcr.io/${{ needs.build-dev.outputs.REPOSITORY }}_dev
+
+    steps:
+      - name: Checkout
+        uses: actions/checkout@v4
+
+      - name: Run ruff
+        run: |
+          ruff check .
+
+      - name: Run mypy
+        run: |
+          mypy .
+
+      - name: Run pytest
+        run: |
+          pytest -v .

.gitignore

@@ -1,15 +1,6 @@
-*.pyc
-addiwraptorepl.py
-build/
-makezip.sh
-nbproject/
-pyMDMix-0.1.6.zip
-pyMDMix.egg-info/
-src/mdmixscore.py
-
-singularity 
-
+# do not save local vscode configuration for now
 .vscode/**
+
 # Byte-compiled / optimized / DLL files
 __pycache__/
 *.py[cod]
@@ -39,12 +30,6 @@ share/python-wheels/
 *.egg
 MANIFEST
 
-# PyInstaller
-#  Usually these files are written by a python script from a template
-#  before PyInstaller builds the exe, so as to inject date/other infos into it.
-*.manifest
-*.spec
-
 # Installer logs
 pip-log.txt
 pip-delete-this-directory.txt
@@ -63,55 +48,16 @@ coverage.xml
 .hypothesis/
 .pytest_cache/
 
-# Translations
-*.mo
-*.pot
-
-# Django stuff:
-*.log
-local_settings.py
-db.sqlite3
-db.sqlite3-journal
-
-# Flask stuff:
-instance/
-.webassets-cache
-
-# Scrapy stuff:
-.scrapy
-
-# Sphinx documentation
-docs/_build/
-
-# PyBuilder
-target/
-
 # Jupyter Notebook
 .ipynb_checkpoints
 
 # IPython
 profile_default/
 ipython_config.py
 
-# pyenv
-.python-version
-
-# pipenv
-#   According to pypa/pipenv#598, it is recommended to include Pipfile.lock in version control.
-#   However, in case of collaboration, if having platform-specific dependencies or dependencies
-#   having no cross-platform support, pipenv may install dependencies that don't work, or not
-#   install all needed dependencies.
-#Pipfile.lock
-
 # PEP 582; used by e.g. github.com/David-OConnor/pyflow
 __pypackages__/
 
-# Celery stuff
-celerybeat-schedule
-celerybeat.pid
-
-# SageMath parsed files
-*.sage.py
 
 # Environments
 .env
@@ -122,20 +68,7 @@ ENV/
 env.bak/
 venv.bak/
 
-# Spyder project settings
-.spyderproject
-.spyproject
-
-# Rope project settings
-.ropeproject
-
-# mkdocs documentation
-/site
-
 # mypy
 .mypy_cache/
 .dmypy.json
 dmypy.json
-
-# Pyre type checker
-.pyre/

Dockerfile

@@ -1,21 +1,22 @@
-FROM ggutierrezbio/ambertools20
-ARG CONDA_PREFIX="/opt/SOFT/miniconda3"
-ENV PATH="$CONDA_PREFIX/bin:${PATH}"
-ARG PATH="$CONDA_PREFIX/bin:${PATH}"
-
-SHELL [ "/bin/bash", "--login", "-c" ]
-RUN apt-get update && apt-get install -y wget git && rm -rf /var/lib/apt/lists/*
-
-RUN wget \
-    https://repo.anaconda.com/miniconda/Miniconda3-latest-Linux-x86_64.sh \
-    && bash Miniconda3-latest-Linux-x86_64.sh -b -p $CONDA_PREFIX \
-    && rm -f Miniconda3-latest-Linux-x86_64.sh 
-RUN conda --version
-
-COPY ./environment_p27.yml ./environment_p27.yml
-RUN conda env create -f environment_p27.yml
-RUN echo ". $CONDA_PREFIX/etc/profile.d/conda.sh" >> ~/.bash_profile
-RUN echo "conda activate mdmix-env" >> ~/.bash_profile
-WORKDIR /mnt
-SHELL ["conda", "run", "-n", "mdmix-env", "/bin/bash", "-c"]
-ENTRYPOINT ["conda", "run", "-n", "mdmix-env", "mdmix"]
+FROM continuumio/miniconda3 as base
+
+ARG PYTHON_VERSION=3.12
+
+# Create environment and install ambertools
+RUN conda config --add channels defaults && \
+    conda config --add channels bioconda && \
+    conda config --add channels conda-forge
+
+# RUN apt update && apt install libnetcdf-dev -y
+
+RUN conda install -y python=${PYTHON_VERSION} ambertools
+
+COPY requirements.txt .
+RUN pip install --no-cache-dir -r requirements.txt
+
+CMD ["bash"]
+
+FROM base AS development
+
+COPY requirements-dev.txt .
+RUN python -m pip install -r requirements-dev.txt

README.md

@@ -1,76 +1 @@
-## pyMDMix --- http://mdmix.sourceforge.net
-
-The program is distributed under GNU GPLv3 license. Find the license file
-under Licenses/ folder.
-
-DOCUMENTATION
-=============
-All documentation on program usage is online at
-http://mdmix.sourceforge.net
-
-INSTALLATION
-============
-
-1- Dependencies
----------------
-This version of pyMDMix depends on:
-  - ambertools>=12
-  - python>=2.7
-
-make sure ambertools environment variables are set
-
-2 - Installation process
-------------------------
-it is advised to install pyMDMix in a virtual environment
-
-there are three recommended ways to install pyMDMix:
-1. from the repository by
-`python -m pip install [insert address here]`
-
-2. from the project's local folder after cloning the repo by
-`python -m pip install .`
-
-3. Use conda or mamba: we will first create the correct conda environment which will already contain ambertools. We will then set the AMBERHOME variable within the environment and finally proceed to install pymdmix from the local git cloned files. Make sure `$CONDA_PREFIX` points to the conda installation directory (it may happen when you activate the new environment this varaible is lost, in that case change the variable for the explicit path). 
-
-```bash
-git clone https://github.com/CBDD/pyMDmix.git
-cd pyMDMix
-conda env create -f environment_p27.yml
-conda activate mdmix-env
-conda env config vars set AMBERHOME=$CONDA_PREFIX/envs/mdmix-env
-pip install .
-```
-
-3 - Testing
------------
-
-You can test the package has been successfuly installed by activating
-the environment and, from a folder other than the cloned repository, running
-`python -m pyMDMix`
-if everything went fine, you will see something like
-`Welcome to MDMix 2.6`
-
-The main script should have been installed correclty also. check it by running
-`mdmix -h`
-
-Test the program works correctly:
-	Move again to the package source directory and type:
-		> python pyMDMix/test.py all
-	This will run a series of source code checks.
-	No test should fail.
-
-4 - Using Docker
-----------------
-Build and run from a docker container using the provided Dockerfile.
-
-- docker build -t pymdmix .
-- docker run -v $PWD:/mnt pymdmix -h
-
-The docker run command will mount the current working directory (windows users should replace $PWD by %cd%) so the container has access to the current location. Output will be also in the current working directory. 
-s
-
-4 - Enjoy!
-----------
-Read program usage at online documentation.
-
-
+# pyMDMix