Add dependencies for pyproject.toml (#84)

.github/workflows/python-package.yml

@@ -24,21 +24,23 @@ jobs:
       with:
         miniconda-version: "latest"
         mamba-version: "*"
-        environment-file: conda/environment.yaml
+        environment-file: conda/dev.yaml
         channels: conda-forge,nodefaults
         activate-environment: env-pysus
         use-mamba: true
         miniforge-variant: Mambaforge
 
-    - name: Install dependencies
+    - name: Install Dependencies
       run: |
-        make install
+        curl -sSL https://raw.githubusercontent.com/python-poetry/poetry/master/get-poetry.py | python -
+        export PATH="$HOME/.poetry/bin:$PATH"
+        poetry config virtualenvs.create false && poetry build && poetry install
 
     - name: Lint with flake8
       run: |
         make check-codestyle
 
-    - name: build and deploy jupyterlab
+    - name: Run jupyterlab with PySUS
       run: |
         make run-jupyter-pysus
 

.gitignore

@@ -18,3 +18,4 @@ pyvenv.cfg
 *.jupyter/
 *.local/
 *.mozilla/
+*.ipynb_checkpoints*

.pre-commit-config.yaml

@@ -8,10 +8,12 @@ repos:
       hooks:
         - id: isort
 
-    - repo: https://github.com/psf/black
-      rev: 21.9b0
-      hooks:
-        - id: black
+    -   repo: https://github.com/psf/black
+        rev: 22.3.0
+        hooks:
+        -   id: black
+            exclude: ^dist/
+
 
     - repo: https://gitlab.com/pycqa/flake8
       rev: 3.9.2

MANIFEST.in

@@ -1,4 +1,3 @@
 recursive-include pysus *.c *.h
 include pysus/utilities/*
-include pysus/utilities/c-src/*
 include requirements.txt

Makefile

@@ -1,4 +1,7 @@
-SHELL=/bin/bash
+SHELL := /usr/bin/env bash
+PYTHON := python
+PYTHONPATH := ${PWD}
+
 
 .PHONY: clean clean-test clean-pyc clean-build help
 .DEFAULT_GOAL := help
@@ -22,15 +25,24 @@ DOCKER = docker-compose -p pysus -f docker/docker-compose.yaml
 SERVICE :=
 
 
+#* Poetry
+.PHONY: poetry-download
+poetry-download:
+	curl -sSL https://raw.githubusercontent.com/python-poetry/poetry/master/install-poetry.py | $(PYTHON) -
+
+.PHONY: poetry-remove
+poetry-remove:
+	curl -sSL https://raw.githubusercontent.com/python-poetry/poetry/master/install-poetry.py | $(PYTHON) - --uninstall
+
 #* Installation
 .PHONY: install
-install: clean ## install the package to the active Python's site-packages
-	python setup.py install
+install:
+	poetry lock -n && poetry export --without-hashes > requirements.txt
+	poetry build && poetry install
 
 .PHONY: pre-commit-install
-develop-install: clean ## install the package in development mode
-	pip install -e '.[dev]'
-	pre-commit install
+pre-commit-install:
+	poetry run pre-commit install
 
 #* Linting
 .PHONY: check-codestyle
@@ -56,7 +68,7 @@ test-jupyter-pysus: ## run pytest for notebooks inside jupyter container
 
 .PHONY: test
 test: ## run tests quickly with the default Python
-	py.test
+	poetry run pytest -vv pysus/tests/
 
 coverage: ## check code coverage quickly with the default Python
 	coverage run --source pysus/tests/ -m pytest
@@ -79,6 +91,7 @@ clean-build: ## remove build artifacts
 	find . -name '*.mozilla' -exec rm -fr {} +
 	find . -name '*.egg-info' -exec rm -fr {} +
 	find . -name '*.egg' -exec rm -f {} +
+	find . -name '*.ipynb_checkpoints' -exec rm -rf {} +
 
 .PHONY: clean-pyc
 clean-pyc: ## remove Python file artifacts

conda/dev.yaml

@@ -0,0 +1,12 @@
+name: env-pysus
+channels:
+  - conda-forge
+  - nodefaults
+dependencies:
+  - cffi
+  - docker-compose
+  - gcc
+  - make
+  - pip
+  - psycopg2
+  - python 3.9.*

docker/Dockerfile

@@ -6,40 +6,47 @@ USER root
 
 ENV DEBIAN_FRONTEND=noninteractive
 
+ENV HOME "/home/pysus"
+ENV PATH "$PATH:/home/pysus/.local/bin"
+ENV ENV_NAME base
+ENV PATH "/opt/conda/envs/$ENV_NAME/bin:$PATH"
+ENV PATH "/opt/poetry/bin:$PATH"
+
 RUN apt-get -qq update --yes \
   && apt-get -qq install --yes --no-install-recommends \
   build-essential firefox\
-  ca-certificates sudo \
+  ca-certificates sudo curl \
   && rm -rf /var/lib/apt/lists/*
 
-RUN useradd -ms /bin/bash developer \
-  && echo "developer ALL=(ALL) NOPASSWD: ALL" > /etc/sudoers.d/developer \
-  && chmod 0440 /etc/sudoers.d/
-
-# Set home to developer
-ENV HOME /home/developer
-# Allow the application to execute as any UID 
-# and still write temporary data to /tmp
-ENV APP_TMP_DATA=/tmp
-
-# Copy environment file to tmp/
-COPY conda/environment.yaml ${APP_TMP_DATA}/environment.yaml
-# Executable in a container to be owned by the root user
-COPY docker/test_notebooks.sh /test_notebooks.sh
-COPY docker/entrypoint.sh /entrypoint.sh
-
-# Use environment to update the env base
-RUN mamba update --all --yes --quiet \
-  && mamba env update --file ${APP_TMP_DATA}/environment.yaml --name base \
+RUN useradd -ms /bin/bash pysus \
+  && echo "pysus ALL=(ALL) NOPASSWD: ALL" > /etc/sudoers.d/pysus \
+  && chmod 0440 /etc/sudoers.d/ \
+  && echo 'source /opt/conda/bin/activate "$ENV_NAME" && exec "$@"' > /activate.sh \
+  && echo 'source activate "$ENV_NAME"' >  /home/pysus/.bashrc \
+  && chmod +x /activate.sh \
+  && chmod -R a+rwx /opt/conda /tmp \
+  && sudo chown -R pysus:pysus /usr/src
+
+COPY --chown=pysus:pysus conda/dev.yaml /tmp/dev.yaml
+COPY --chown=pysus:pysus docker/entrypoint.sh /entrypoint.sh
+COPY --chown=pysus:pysus pyproject.toml poetry.lock LICENSE README.md /usr/src/
+COPY --chown=pysus:pysus pysus /usr/src/pysus
+COPY --chown=pysus:pysus docs/source/*.ipynb /home/pysus/Notebooks/
+
+RUN curl -sSL https://raw.githubusercontent.com/python-poetry/poetry/master/install-poetry.py | POETRY_HOME=/opt/poetry python && \
+    cd /usr/local/bin && \
+    ln -s /opt/poetry/bin/poetry && \
+    poetry config virtualenvs.create false
+
+RUN chmod -R a+rwx /home/pysus/.config/pypoetry/
+
+USER pysus
+
+RUN mamba env update -n $ENV_NAME \
+    --file /tmp/dev.yaml \
+  && cd /usr/src && poetry build && poetry install \
   && mamba clean -afy
 
-USER developer
-
-# Copy only notebooks to the container with permissions to user
-RUN mkdir ${HOME}/Notebooks
-WORKDIR ${HOME}/Notebooks
-COPY pysus/Notebooks .
-
-ENTRYPOINT ["/entrypoint.sh"]
+WORKDIR /home/pysus/Notebooks
 
-CMD ["/usr/bin/firefox"]
+ENTRYPOINT ["bash", "/activate.sh"]

docker/docker-compose.yaml

@@ -11,3 +11,5 @@ services:
       - DISPLAY=:0
     volumes:
       - /tmp/.X11-unix:/tmp/.X11-unix
+    entrypoint: ["/entrypoint.sh"]
+    command: ["/usr/bin/firefox"]