feat: add Dockerfile (#10)

* feat: add Dockerfile (#6)

* feat: update ci with docker #6

.dockerignore

@@ -0,0 +1,8 @@
+*
+!scRNAsim_toolz/
+!tests/
+!setup.py
+!requirements.txt
+!environment.yml
+!LICENSE
+!README.md

.github/workflows/ci.yml

@@ -85,4 +85,40 @@ jobs:
           token: ${{ secrets.CODECOV_TOKEN }}
           files: ./coverage.xml
           verbose: true
-          fail_ci_if_error: false
+          fail_ci_if_error: false
+
+  publish:
+    name: build and publish app image
+    runs-on: ubuntu-latest
+    if: |
+      github.event_name == 'push' && 
+      github.ref == format('refs/heads/{0}', github.event.repository.default_branch)
+
+    steps:
+
+      - name: check out repository
+        uses: actions/checkout@v4
+
+      - name: generate tag
+        run: |
+          echo "TAG=$(date '+%Y%m%d')" >> $GITHUB_ENV
+
+      - name: build and publish image
+        id: docker
+        uses: philips-software/[email protected]
+        with:
+          dockerfile: .
+          image-name: "scrnasim-toolz"
+          tags: "latest ${{ env.TAG }}"
+          push-branches: "${{ github.event.repository.default_branch }}"
+        env:
+          REGISTRY_USERNAME: ${{ secrets.DOCKERHUB_LOGIN }}
+          REGISTRY_TOKEN: "${{ secrets.DOCKERHUB_TOKEN }}"
+          DOCKER_ORGANIZATION: ${{ secrets.DOCKERHUB_ORG }}
+          GITHUB_ORGANIZATION: ${{ github.repository_owner }}
+
+      - name: Verify that image was pushed
+        run: |
+          echo "Push indicator: ${{ steps.docker.outputs.push-indicator }}"
+          echo "# Set to 'true' if image was pushed, empty string otherwise"
+          test "${{ steps.docker.outputs.push-indicator }}" == "true"

Dockerfile

@@ -0,0 +1,39 @@
+###### BASE IMAGE ######
+FROM continuumio/miniconda3:4.12.0
+
+####### METADATA #######
+LABEL base_image="continuumio/miniconda3:4.12.0"
+LABEL version="1.0"
+LABEL software="scRNAsim-toolz"
+LABEL software.version="v0.1.1"
+LABEL about.home="https://github.com/zavolanlab/scRNAsim-toolz"
+
+###### MAINTAINER ######
+LABEL maintainer="Máté Balajti <[email protected]>"
+
+##### INSTALLATION #####
+
+# COPY THE YAML & INSTALL SOFTWARE WITH CONDA
+WORKDIR /usr/src/app
+COPY ./ ./
+RUN conda env create --file environment.yml
+
+# VARIABLES
+ARG WORKDIR="/home/USER"
+ARG USER="USER"
+ARG GROUP="GROUP"
+ENV PATH="${WORKDIR}:${PATH}"
+
+# CREATE USER
+RUN groupadd -r ${GROUP} && useradd --no-log-init -r -g ${GROUP} ${USER}
+
+# SET ENVIRONMENT
+WORKDIR ${WORKDIR}
+RUN chown -R ${USER}:${GROUP} ${WORKDIR} && chmod 700 ${WORKDIR}
+USER ${USER}
+RUN echo "source activate scrnasim" > ~/.bashrc
+ENV PATH /opt/conda/envs/scrnasim/bin:$PATH
+
+# SET ENTRYPOINT
+ENTRYPOINT ["transcript-sampler"]
+CMD ["-v"]

environment-dev.yml

@@ -10,5 +10,3 @@ dependencies:
   - mypy
   - pylint
   - pytest
-  - pip:
-    - -e .

environment.yml

@@ -3,13 +3,13 @@ channels:
   - conda-forge
   - bioconda
 dependencies:
+  - pip>=20.2.3
   - biopython>=1.78
   - polars==0.16.17
   - gtfparse
   - numpy>=1.23.3
   - nextflow
   - pandas>=1.4.4
-  - pip>=20.2.3
   - python>=3.6, <=3.10
   - pyarrow
   - pip:

pull_request_template.md

@@ -0,0 +1,43 @@
+### Description
+
+Please include a summarized description of the change(s) and which issue(s)
+this pull request addresses, if any. Please include relevant motivation and
+context, unless already duly described in an associated issue or resource.
+Make sure to list any dependencies that are required for this change.
+
+Fixes # (issue)
+
+### Type of change
+
+Please delete options that are not relevant.
+
+- [ ] Bug fix (non-breaking change which fixes an issue)
+- [ ] New feature (non-breaking change which adds functionality)
+- [ ] Breaking change (fix or feature that would cause existing functionality
+      to not work as expected)
+- [ ] Documentation update
+
+### Checklist
+
+Please carefully read these items and tick them off if the statements are true
+_or do not apply_.
+
+- [ ] I have performed a self-review of my own code
+- [ ] My code follows the existing coding style, lints and generates no new
+      warnings
+- [ ] I have added type annotations to all function/method signatures, and I
+      have added type annotations for any local variables that are non-trivial,
+      potentially ambiguous or might otherwise benefit from explicit typing.
+- [ ] I have commented my code in hard-to-understand areas
+- [ ] I have added ["Google-style docstrings"] to all new modules, classes,
+      methods/functions or updated previously existing ones
+- [ ] I have added tests that prove my fix is effective or that my feature
+      works
+- [ ] New and existing unit tests pass locally with my changes and I have not
+      reduced the code coverage relative to the previous state
+- [ ] I have updated any sections of the app's documentation that are affected
+      by the proposed changes
+
+If for some reason you are unable to tick off all boxes, please leave a
+comment explaining the issue you are facing so that we can work on it
+together.

requirements.txt

@@ -4,5 +4,5 @@ pandas>=1.4.4
 polars==0.16.17
 gtfparse
 setuptools
-cli_test_helpers
 pyarrow
+cli_test_helpers