Merge pull request #15 from alexpron/packaging

Installation mechanism and basic CI.
That worked like a charm for me.

.github/workflows/conda-installation.yml

@@ -0,0 +1,41 @@
+name: Python installation
+
+on: [push]
+
+jobs:
+  build:
+    strategy:
+      matrix:
+        os: [ubuntu-latest]
+        python-version: ["3.8", "3.9", "3.10"]
+        #TODO: use github action to read python version from pyproject.toml
+    runs-on:  ${{ matrix.os }}
+    steps:
+      - uses: actions/checkout@v4
+      - name: Setup Python
+        uses: conda-incubator/setup-miniconda@v3
+        with:
+          auto-update-conda: true
+          activate-environment: working-env
+          python-version: ${{ matrix.python-version }}
+          auto-activate-base: false
+      - name: Install dependencies
+        shell:  bash -el {0}
+        run: |
+          conda config --set pip_interop_enabled True
+          python -m pip install .
+          conda update --all
+          conda install -c conda-forge heudiconv bids-validator dcm2niix git-annex=*=alldep* datalad 
+
+      # Create virtual env under each python version
+      # (optional and a bit redundant because we are already on a specific python)
+      # it insures installation instruction provided in README are working
+#      - name: Test with pytest
+#        run: pytest tests.py --doctest-modules --junitxml=junit/test-results-${{ matrix.python-version }}.xml
+#      - name: Upload pytest test results
+#        uses: actions/upload-artifact@v4
+#        with:
+#          name: pytest-results-${{ matrix.python-version }}
+#          path: junit/test-results-${{ matrix.python-version }}.xml
+#        # Use always() to always run this step to publish test results when there are test failures
+#        if: ${{ always() }}

.github/workflows/pip-installation.yml

@@ -0,0 +1,36 @@
+name: Python installation
+
+on: [push]
+
+jobs:
+  build:
+    strategy:
+      matrix:
+        os: [ubuntu-latest]
+        python-version: ["3.8", "3.9", "3.10"]
+        #TODO: use github action to read python version from pyproject.toml
+    runs-on:  ${{ matrix.os }}
+    steps:
+      - uses: actions/checkout@v4
+      - name: Setup Python # Set Python version
+        uses: actions/setup-python@v5
+        with:
+          python-version: ${{ matrix.python-version }}
+      # Create virtual env under each python version
+      # (optional and a bit redundant because we are already on a specific python)
+      # it insures installation instruction provided in README are working
+      - name: Install dependencies
+        run: |
+          python -m venv working-env --clear
+          source working-env/bin/activate
+          python -m pip install --upgrade pip
+          python -m pip install -e .
+#      - name: Test with pytest
+#        run: pytest tests.py --doctest-modules --junitxml=junit/test-results-${{ matrix.python-version }}.xml
+#      - name: Upload pytest test results
+#        uses: actions/upload-artifact@v4
+#        with:
+#          name: pytest-results-${{ matrix.python-version }}
+#          path: junit/test-results-${{ matrix.python-version }}.xml
+#        # Use always() to always run this step to publish test results when there are test failures
+#        if: ${{ always() }}

Readme.md → README.md

@@ -8,14 +8,28 @@ The scripts `convert_dicoms_to_niftis.py` and `create_previews.py` enable to con
 
 ## Install
 
-It is advised to install the project in [a virtual environment](https://docs.python.org/3/tutorial/venv.html). 
-
-[Install python with pip](https://www.python.org/downloads/) ; then use `pip install -r requirements.txt` to install python dependencies.
+It is advised to install the project in python virtual environment relying either on [venv](https://docs.python.org/3/tutorial/venv.html) or preferably  [(mini)conda](https://conda.io/projects/conda/en/latest/user-guide/tasks/manage-environments.html)
+### Installation with pip 
+[Install python with pip](https://www.python.org/downloads/) ; then use `pip install .` to install python dependencies.
 
 Optionally, rename the `.env.example` to `.env` and set the variables (`shanoir_password`, `gpg_recipient`) to your needs.
 
 *See the "Installing DicomAnonymizer" section if you want to use DicomAnonymizer for the dicom anonymization instead of PyDicom.*
 
+### Installation with conda
+> [!IMPORTANT]
+> This installation method is required if shanoir2bids.py is used 
+
+In an active conda virtual environment type 
+```bash
+#use pip packages as dependencies
+conda config --set pip_interop_enabled True
+pip install . 
+#replace pip packages with conda packages when equivalent
+conda update --all
+# install missing conda packages (far simpler than using pip)
+conda install -c conda-forge heudiconv git-annex=*=alldep* datalad
+```
 ## Usage
 
 There are three scripts to download datasets:

pyproject.toml

@@ -0,0 +1,49 @@
+[build-system]
+requires = ["setuptools>=64", "setuptools_scm>=8"]
+build-backend = "setuptools.build_meta"
+
+[project]
+name = "shanoir-downloader"
+version = "0.0.1"
+
+dynamic = ["dependencies", "optional-dependencies"]
+
+requires-python = ">=3.8, <3.11"
+
+authors = [
+  {name = "Arthur Masson",email = "[email protected]"},
+  {name = "Quentin Duché", email = "[email protected]"},
+  {name = "Malo Gaubert", email = "[email protected]"},
+]
+maintainers = [
+  {name = "Quentin Duché", email = "[email protected]"}
+]
+description = "Download Shanoir Datasets in various format using Python"
+readme = "README.md"
+license = {file = "LICENSE"}
+keywords = ["Shanoir", "DICOM", "NIFTI", "BIDS"]
+classifiers = [
+  "Programming Language :: Python"
+]
+
+[project.urls]
+Repository = "https://github.com/Inria-Empenn/shanoir_downloader.git"
+"Bug Tracker" = "https://github.com/Inria-Empenn/shanoir_downloader/issues"
+Changelog = "https://github.com/Inria-Empenn/shanoir_downloader/blob/master/CHANGELOG.md"
+
+[tool.setuptools]
+py-modules = []
+
+[tool.setuptools_scm]
+
+[tool.setuptools.dynamic]
+dependencies = {file = ["requirements.txt"]}
+
+
+#optional-dependencies = {dev = { file = ["requirements-dev.txt"] }}
+#[project.scripts]
+#spam-cli = "shanoir-downloader:main_cli"
+
+#
+#[project.entry-points."spam.magical"]
+#tomatoes = "spam:main_tomatoes"