Merge branch 'main' into readme-clean-up

Author: fccoelho

.github/workflows/python-package.yml

@@ -13,7 +13,7 @@ jobs:
 
     strategy:
       matrix:
-        python_version: ["3.10", "3.11"]
+        python_version: ["3.10", "3.11", "3.12", "3.13"]
 
     concurrency:
       group: ci-tests-${{ matrix.python_version }}-${{ github.ref }}
@@ -24,19 +24,21 @@ jobs:
 
     - uses: conda-incubator/setup-miniconda@v3
       with:
-        miniconda-version: "latest"
-        mamba-version: "*"
+        miniforge-version: latest
         environment-file: conda/dev.yaml
         channels: conda-forge,nodefaults
         activate-environment: pysus
-        use-mamba: true
-        miniforge-variant: Mambaforge
+        auto-update-conda: true
+        conda-solver: libmamba
 
     - name: Run jupyterlab with PySUS
       run: |
         make run-jupyter-pysus
+        # make test-jupyter-pysus  ## takes too long
 
-    - name: Test with pytest
+    - name: Linting & Tests
       run: |
+        export CI=1
         poetry install
+        pre-commit run --all-files
         make test-pysus

.github/workflows/release.yaml

@@ -20,13 +20,12 @@ jobs:
 
     - uses: conda-incubator/setup-miniconda@v3
       with:
-        miniconda-version: "latest"
-        mamba-version: "*"
+        miniforge-version: latest
         environment-file: conda/dev.yaml
         channels: conda-forge,nodefaults
         activate-environment: pysus
-        use-mamba: true
-        miniforge-variant: Mambaforge
+        auto-update-conda: true
+        conda-solver: libmamba
 
     - uses: actions/setup-node@v3
       with:

.idea/PySUS.iml

@@ -1,3 +1,5 @@
+default_stages: [commit, push]
+
 repos:
   - repo: https://github.com/pre-commit/pre-commit-hooks
     rev: v4.1.0
@@ -16,8 +18,6 @@ repos:
       files: ""
       language: system
       pass_filenames: true
-      stages:
-        - commit
       types:
         - python
         - file
@@ -30,8 +30,6 @@ repos:
       language: python
       name: flake8
       pass_filenames: true
-      stages:
-        - commit
       types:
         - python
 
@@ -42,7 +40,5 @@ repos:
       language: python
       name: isort
       pass_filenames: true
-      stages:
-        - commit
       types:
         - python

.idea/misc.xml

@@ -1,6 +1,22 @@
 Release Notes
 ---
 
+## [1.0.0](https://github.com/AlertaDengue/PySUS/compare/0.15.0...1.0.0) (2025-06-11)
+
+### ⚠ BREAKING CHANGES
+
+* **package:** release for py3.13 (#223)
+
+### Features
+
+* **package:** release for py3.13 ([#223](https://github.com/AlertaDengue/PySUS/issues/223)) ([c6008f4](https://github.com/AlertaDengue/PySUS/commit/c6008f41b55bc65e98b45adcbb6e8f304732928e))
+
+## [0.15.0](https://github.com/AlertaDengue/PySUS/compare/0.14.3...0.15.0) (2024-12-03)
+
+### Features
+
+* **package:** bump version to 0.15.0 ([#216](https://github.com/AlertaDengue/PySUS/issues/216)) ([8ed64be](https://github.com/AlertaDengue/PySUS/commit/8ed64be381531306152edf0aa7c57711fff4b293))
+
 ## [0.14.3](https://github.com/AlertaDengue/PySUS/compare/0.14.2...0.14.3) (2024-07-31)
 
 ### Bug Fixes

.pre-commit-config.yaml

@@ -22,7 +22,7 @@ export PRINT_HELP_PYSCRIPT
 help:
 	@python -c "$$PRINT_HELP_PYSCRIPT" < $(MAKEFILE_LIST)
 
-DOCKER = docker-compose -p pysus -f docker/docker-compose.yaml
+DOCKER = docker compose -p pysus -f docker/docker-compose.yaml
 SERVICE :=
 SEMANTIC_RELEASE = npx --yes \
           -p semantic-release \
@@ -48,12 +48,11 @@ down-jupyter-pysus: ## stop and remove containers for all services
 #* Tests
 .PHONY: test-jupyter-pysus
 test-jupyter-pysus: ## run pytest for notebooks inside jupyter container
-	$(DOCKER) exec -T jupyter bash /test_notebooks.sh
+	$(DOCKER) exec -T jupyter pytest -vv --nbmake
 
 .PHONY: test-pysus
 test-pysus: ## run tests quickly with the default Python
-	cp docs/source/**/*.ipynb pysus/Notebooks
-	poetry run pytest -vv pysus/tests/
+	poetry run pytest -vv pysus/tests/ --retries 3 --retry-delay 15
 
 # RELEASE
 # =======

CHANGELOG.md

@@ -55,6 +55,7 @@ First, clone the Pysus repository:
 ```bash
 git clone https://github.com/AlertaDengue/PySUS.git
 ``` 
+
 then from within the PySUS directory build the container
 
 ```bash
@@ -71,7 +72,7 @@ Point your browser to [http://127.0.0.1:8888](http://127.0.0.1:8888) and have fu
 Once you are done, you can stop the container with a simple `ctrl-c` from the terminal you started it or use the following command:
 ```bash
 # to find the container ID
-docker ps 
+docker ps
 docker stop <CONTAINER ID>
 ```
 ### Mounting your working directory in the container
@@ -104,7 +105,7 @@ setx PYSUS_CACHEPATH "C:\Users\Me\desired\path\.pysus"
 In Docker, just add an extra parameter `-e PYSUS_CACHEPATH="/home/me/desired/path/.pysus"` when starting the container:
 
 ```bash
-docker run -p 8888:8888 -e PYSUS_CACHEPATH="/home/me/desired/path/.pysus" pysus:latest 
+docker run -p 8888:8888 -e PYSUS_CACHEPATH="/home/me/desired/path/.pysus" pysus:latest
 ```
 
 ## Examples
@@ -143,7 +144,7 @@ Downloading and reading SINASC data:
 In[1]: from pysus.online_data.SINASC import download
 In[2]: df = download('SE', 2015)
 In[3]: df.head()
-Out[3]: 
+Out[3]:
    NUMERODN        CODINST ORIGEM    ...     TPROBSON PARIDADE KOTELCHUCK
 0  19533794  MSE2805100001      1    ...           11        1          9
 1  52927108  MSE2802700001      1    ...           11        1          9
@@ -159,7 +160,7 @@ Dowloading and reading SIM data:
 In[1]: from pysus.online_data.SIM import download
 In[2]: df = download('ba', 2007)
 In[3]: df.head()
-Out[3]: 
+Out[3]:
    NUMERODO TIPOBITO   DTOBITO  ...   UFINFORM        CODINST CB_PRE
 0  01499664        2  30072007  ...         29  RBA2914800001   C229
 1  09798190        2  04072007  ...         29  RBA2914800001    R98
@@ -175,7 +176,7 @@ Dowloading and reading CIHA data:
 In[1]: from pysus.online_data.CIHA import download
 In[2]: df = download('mg', 2009, 7)
 In[3]: df.head()
-Out[3]: 
+Out[3]:
   ANO_CMPT MES_CMPT ESPEC        CGC_HOSP  ...  CAR_INT HOMONIMO     CNES FONTE
 0     2009       07        16505851000126  ...                    2126796     1
 1     2009       07        16505851000126  ...                    2126796     2
@@ -191,7 +192,7 @@ Dowloading and reading SIA data:
 In[1]: from pysus.online_data.SIA import download
 In[2]: bi, ps = download('AC', 2020, 3, group=["BI", "PS"])
 In[3]: bi.head()
-Out[3]: 
+Out[3]:
     CODUNI  GESTAO CONDIC   UFMUN TPUPS  ... VL_APROV UFDIF MNDIF ETNIA NAT_JUR
 0  2000733  120000     EP  120040    07  ...     24.2     0     0          1023
 1  2001063  120000     EP  120040    36  ...      7.3     0     0          1023
@@ -208,4 +209,3 @@ Out[4]:
 3   2002094  120000     EP  120040  ...               0      0    1023
 4   2002094  120000     EP  120040  ...               0      0    1023
 [5 rows x 45 columns]
-```

Makefile

@@ -3,11 +3,9 @@ channels:
   - conda-forge
   - defaults
 dependencies:
-  - python >=3.10,<3.12
-  - numpy>=1.26.2
-  - cffi
-  - gcc
+  - docker-compose
+  - python>=3.10,<3.14
   - jupyter
   - make
-  - poetry>=1.3.2
+  - poetry
   - pip

README.md

@@ -47,10 +47,10 @@ about:
   home: "https://github.com/fccoelho/PySUS"
   license: gpl-v3
   license_family: GPL3
-  license_file: 
+  license_file:
   summary: "Tools for dealing with Brazil's Public health data"
-  doc_url: 
-  dev_url: 
+  doc_url:
+  dev_url:
 
 extra:
   recipe-maintainers: