feat(IBGE): continue work of AlertaDengue #192 (#193)

* Started the implementation of fetching the population estimates from DATASUS

* Added missing path

* Fixed many bugs.
testing passing for sources POPTCU and projpop

* feat(IBGE): continue work of #192

* fix get_files from IBGEDATASUS

* finish get_population

* clean & update a the worflows

* fix tests

---------

Co-authored-by: Flávio Codeço Coelho <[email protected]>

Author: luabida

.github/workflows/python-package.yml

@@ -20,14 +20,9 @@ jobs:
       cancel-in-progress: true
 
     steps:
-    - uses: actions/checkout@v3
+    - uses: actions/checkout@v4
 
-    - name: Prepare conda environment
-      run: |
-        sed -i s/python\ 3\.11/python\ ${{ matrix.python_version }}/ conda/dev.yaml
-        cat conda/dev.yaml
-
-    - uses: conda-incubator/setup-miniconda@v2
+    - uses: conda-incubator/setup-miniconda@v3
       with:
         miniconda-version: "latest"
         mamba-version: "*"
@@ -37,27 +32,11 @@ jobs:
         use-mamba: true
         miniforge-variant: Mambaforge
 
-
-    - name: Install dependencies
-      run: |
-        curl -sSL https://install.python-poetry.org/ | python -
-        export PATH="$HOME/.poetry/bin:$PATH"
-        poetry config virtualenvs.create false
-
-    - name: Install main dependencies
-      run: |
-        make conda-install-main ENVCREATE=conda-env
-
-    - name: Lint with flake8
-      run: |
-        make conda-install-dev
-        make check-codestyle
-
     - name: Run jupyterlab with PySUS
       run: |
         make run-jupyter-pysus
 
     - name: Test with pytest
       run: |
-        make conda-install-geo
+        poetry install
         make test-pysus

.github/workflows/release.yaml

@@ -16,9 +16,9 @@ jobs:
         shell: bash -l {0}
 
     steps:
-    - uses: actions/checkout@v2
+    - uses: actions/checkout@v4
 
-    - uses: conda-incubator/setup-miniconda@v2
+    - uses: conda-incubator/setup-miniconda@v3
       with:
         miniconda-version: "latest"
         mamba-version: "*"
@@ -46,4 +46,3 @@ jobs:
       run: |
         poetry config pypi-token.pypi ${PYPI_TOKEN}
         make release
-

.gitignore

@@ -1,4 +1,4 @@
-.idea
+.idea/
 PySUS.egg-info/
 build/
 dist/

.idea/PySUS.iml

@@ -36,42 +36,6 @@ SEMANTIC_RELEASE = npx --yes \
           -p "semantic-release-replace-plugin" \
           semantic-release
 
-
-# Create a Conda environment and install dependencies for development.
-.PHONY: conda-env
-conda-env:
-	mamba env create -f conda/dev.yaml --force
-
-# Install main project dependencies using Poetry.
-.PHONY:  conda-install-main
-conda-install-main: ${ENVCREATE}
-	conda run -n pysus poetry install --only main
-
-.PHONY: conda-install-dev
-conda-install-dev:
-	conda run -n pysus poetry install --only dev
-
-.PHONY: conda-install-docs
-conda-install-docs:
-	conda run -n pysus poetry install --only docs
-
-.PHONY: conda-install-geo
-conda-install-geo:
-	conda run -n pysus pip install --no-use-pep517 shapely==1.8.5.post1
-	conda run -n pysus poetry install --only geo
-
-# Linting
-.PHONY: pre-commit-install
-pre-commit-install:
-	poetry run pre-commit install
-
-.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
@@ -91,44 +55,6 @@ test-pysus: ## run tests quickly with the default Python
 	cp docs/source/**/*.ipynb pysus/Notebooks
 	poetry run pytest -vv pysus/tests/
 
-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/
-	rm -fr .eggs/
-	find . -name '*.cache' -exec rm -fr {} +
-	find . -name '*.jupyter' -exec rm -fr {} +
-	find . -name '*.local' -exec rm -fr {} +
-	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
-	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
-
-
 # RELEASE
 # =======
 

.idea/misc.xml

@@ -162,7 +162,7 @@
 # Add any paths that contain custom static files (such as style sheets) here,
 # relative to this directory. They are copied after the builtin static files,
 # so a file named "default.css" will overwrite the builtin "default.css".
-html_static_path = ["_static"]
+# html_static_path = ["_static"]
 
 # Add any extra paths that contain custom files (such as robots.txt or
 # .htaccess) here, relative to this directory. These files are copied