Merge pull request #77 from fccoelho/remove_demography

Remove demography

.github/workflows/python-package.yml

@@ -1,32 +1,31 @@
-# This workflow will install Python dependencies, run tests and lint with a variety of Python versions
-# For more information see: https://help.github.com/actions/language-and-framework-guides/using-python-with-github-actions
+name: tests
 
-name: Python package
-
-on:
-  push:
-    branches: [ master ]
-  pull_request:
-    branches: [ master ]
+on: [push, pull_request]
 
 jobs:
   build:
-
     runs-on: ubuntu-latest
     timeout-minutes: 60
+    strategy:
+      matrix:
+        python-version: ["3.9"]
+    concurrency:
+      group: ci-${{ github.ref }}
+      cancel-in-progress: true
+
     defaults:
       run:
         shell: bash -l {0}
 
     steps:
     - uses: actions/checkout@v2
-
+    
     - uses: conda-incubator/setup-miniconda@v2
       with:
         miniconda-version: "latest"
         mamba-version: "*"
-        environment-file: environment.yaml
-        channels: conda-forge
+        environment-file: conda/environment.yaml
+        channels: conda-forge,nodefaults
         activate-environment: env-pysus
         use-mamba: true
         miniforge-variant: Mambaforge
@@ -37,17 +36,12 @@ jobs:
 
     - name: Lint with flake8
       run: |
-        make lint
+        make check-codestyle
 
     - name: build and deploy jupyterlab
       run: |
-        make run_jupyter_pysus
+        make run-jupyter-pysus
 
-    - name: run tests for notebooks on container
+    - name: Test with pytest
       run: |
-        make test_jupyter_pysus
-
-    # - name: Test with pytest
-    #   shell: bash -l {0}
-    #   run: |
-    #     make test
+        make test

Makefile

@@ -21,18 +21,54 @@ help:
 DOCKER = docker-compose -p pysus -f docker/docker-compose.yaml
 SERVICE :=
 
-# Docker basic
-run_jupyter_pysus: ## build and deploy all containers
+
+#* Installation
+.PHONY: install
+install: clean ## install the package to the active Python's site-packages
+	python setup.py install
+
+.PHONY: pre-commit-install
+develop-install: clean ## install the package in development mode
+	pip install -e '.[dev]'
+	pre-commit install
+
+#* Linting
+.PHONY: check-codestyle
+check-codestyle: ## check style with flake8
+	# stop the build if there are Python syntax errors or undefined names
+	flake8 . --count --select=E9,F63,F7,F82 --show-source --statistics
+	# exit-zero treats all errors as warnings. The GitHub editor is 127 chars wide
+	flake8 . --count --exit-zero --max-complexity=10 --max-line-length=127 --statistics
+
+#* Docker basic
+.PHONY: run-jupyter-pysus
+run-jupyter-pysus: ## build and deploy all containers
 	$(DOCKER) up -d --build
 
-down_jupyter_pysus: ## stop and remove containers for all services
+.PHONY: down-jupyter-pysus
+down-jupyter-pysus: ## stop and remove containers for all services
 	$(DOCKER) down -v --remove-orphans
 
-test_jupyter_pysus: ## run pytest for notebooks inside jupyter container
+#* Tests
+.PHONY: test-jupyter-pysus
+test-jupyter-pysus: ## run pytest for notebooks inside jupyter container
 	$(DOCKER) exec -T jupyter bash /test_notebooks.sh
 
+.PHONY: test
+test: ## run tests quickly with the default Python
+	py.test
+
+coverage: ## check code coverage quickly with the default Python
+	coverage run --source pysus/tests/ -m pytest
+	coverage report -m
+	coverage html
+	$(BROWSER) htmlcov/index.html
+
+# Cleaning
+.PHONY: clean
 clean: clean-build clean-pyc clean-test ## remove all build, test, coverage and Python artifacts
 
+.PHONY: clean-build
 clean-build: ## remove build artifacts
 	rm -fr build/
 	rm -fr dist/
@@ -44,37 +80,16 @@ clean-build: ## remove build artifacts
 	find . -name '*.egg-info' -exec rm -fr {} +
 	find . -name '*.egg' -exec rm -f {} +
 
-
+.PHONY: clean-pyc
 clean-pyc: ## remove Python file artifacts
 	find . -name '*.pyc' -exec rm -f {} +
 	find . -name '*.pyo' -exec rm -f {} +
 	find . -name '*~' -exec rm -f {} +
 	find . -name '__pycache__' -exec rm -fr {} +
 
+.PHONY: clean-test
 clean-test: ## remove test and coverage artifacts
 	rm -fr .tox/
 	rm -f .coverage
 	rm -fr htmlcov/
 	rm -fr .pytest_cache
-
-lint: ## check style with flake8
-	# stop the build if there are Python syntax errors or undefined names
-	flake8 . --count --select=E9,F63,F7,F82 --show-source --statistics
-	# exit-zero treats all errors as warnings. The GitHub editor is 127 chars wide
-	flake8 . --count --exit-zero --max-complexity=10 --max-line-length=127 --statistics
-
-install: clean ## install the package to the active Python's site-packages
-	python setup.py install
-
-develop: clean ## install the package in development mode
-	pip install -e '.[dev]'
-	pre-commit install
-
-test: ## run tests quickly with the default Python
-	py.test
-
-coverage: ## check code coverage quickly with the default Python
-	coverage run --source pysus/tests/ -m pytest
-	coverage report -m
-	coverage html
-	$(BROWSER) htmlcov/index.html

environment.yaml → conda/environment.yaml

@@ -3,21 +3,16 @@ channels:
   - conda-forge
   - nodefaults
 dependencies:
+  - docker-compose
   - jupyterlab 
   - nodejs
   - cffi>=1.0.0
   - dbfread
   - geocoder
   - requests
-  - folium
   - fastparquet
-  - geopandas
   - dask
   - wget
-  - colorcet
-  - datashader
-  - xarray
-  - georasters
   - elasticsearch
   - pyarrow
   # dev
@@ -32,6 +27,4 @@ dependencies:
   - numba
   - pip:
     - nbmake
-    - geobr
-    - facets-overview
     - pysus

condarecipe/pysus/meta.yaml

@@ -23,7 +23,6 @@ requirements:
     - pip
     - python
     - requests
-    - georasters
   run:
     - cffi >=1.0.0
     - dbfread
@@ -33,7 +32,6 @@ requirements:
     - pyarrow
     - python
     - requests
-    - georasters
     - elasticsearch
 
 test:

docker/Dockerfile

@@ -23,7 +23,7 @@ ENV HOME /home/developer
 ENV APP_TMP_DATA=/tmp
 
 # Copy environment file to tmp/
-COPY environment.yaml ${APP_TMP_DATA}/environment.yaml
+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