feat!(v1): python 3.13 release; remove cffi (gcc) dep; update readme; release v1? (#222)

* deps!(v1): python 3.13 release; remove cffi (gcc) dep; update readme; release v1?

* debug

* fix(test): test_vaccine imunizacao url is forbidden to be fetched on CI

* replace numpy dep pin by version range

* replace fastparquet dep pin by version range

Author: luabida

.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 }}
@@ -24,13 +24,12 @@ 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
 
     - name: Run jupyterlab with PySUS
       run: |
@@ -39,6 +38,7 @@ jobs:
 
     - 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:

Makefile

@@ -52,7 +52,7 @@ test-jupyter-pysus: ## run pytest for notebooks inside jupyter container
 
 .PHONY: test-pysus
 test-pysus: ## run tests quickly with the default Python
-	poetry run pytest -vv pysus/tests/
+	poetry run pytest -vv pysus/tests/ --retries 3 --retry-delay 15
 
 # RELEASE
 # =======

README.md

@@ -138,26 +138,6 @@ datetime.date(2016, 4, 1)
 
 ```
 
-**Reading `.dbc` file:**
-
-```python
->>> from pysus.utilities.readdbc import read_dbc
-
->>> df = read_dbc(filename, encoding='iso-8859-1')
->>> df.info()
-<class 'pandas.core.frame.DataFrame'>
-RangeIndex: 1239 entries, 0 to 1238
-Data columns (total 58 columns):
-AP_MVM        1239 non-null object
-AP_CONDIC     1239 non-null object
-AP_GESTAO     1239 non-null object
-AP_CODUNI     1239 non-null object
-AP_AUTORIZ    1239 non-null object
-AP_CMP        1239 non-null object
-AP_PRIPAL     1239 non-null object
-AP_VL_AP      1239 non-null float64
-...
-```
 Downloading and reading SINASC data:
 
 ```python

conda/dev.yaml

@@ -4,11 +4,8 @@ channels:
   - defaults
 dependencies:
   - docker-compose
-  - python >=3.10,<3.12
-  - numpy>=1.26.2
-  - cffi
-  - gcc
+  - python>=3.10,<3.14
   - jupyter
   - make
-  - poetry>=1.3.2
+  - poetry
   - pip

docker/docker-compose.yaml

@@ -9,6 +9,7 @@ services:
     privileged: true
     environment:
       - DISPLAY=:0
+      - CI=${CI:-0}
     volumes:
       - /tmp/.X11-unix:/tmp/.X11-unix
     entrypoint: ["/entrypoint.sh"]

poetry.lock

@@ -8,12 +8,11 @@ license = "GPL"
 packages = [{include='pysus'}]
 
 [tool.poetry.dependencies]
-python = ">=3.10,<3.13"
+python = ">=3.10,<3.14"
 python-dateutil = "2.8.2"
-cffi = "1.15.1"
 dbfread = "2.0.7"
-fastparquet = ">=2023.10.1"
-numpy = "1.26.2"
+fastparquet = ">=2023.10.1,<=2024.11.0"
+numpy = ">1,<3"
 pyarrow = ">=11.0.0"
 pycparser = "2.21"
 pyreaddbc = ">=1.1.0"
@@ -39,6 +38,7 @@ isort = "^5.10.1"
 pre-commit = "^2.20.0"
 pytest-timeout = "^2.1.0"
 nbsphinx = "^0.9.3"
+pytest-retry = "1.7.0"
 
 [tool.poetry.group.docs.dependencies]
 sphinx = "^5.1.1"

pyproject.toml

@@ -107,8 +107,6 @@ def elasticsearch_fetch(uri, auth, json_body={}):
             print(resp)
         total += len(resp["hits"]["hits"])
         print(f"Downloaded {total} records\r", end="")
-        # print(resp)
-        # print(uri)
         yield [h["_source"] for h in resp["hits"]["hits"]]
         if "_scroll_id" in resp:
             scroll_id = resp["_scroll_id"]

pysus/online_data/vaccine.py

@@ -1,3 +1,4 @@
+import os
 import unittest
 
 import pandas as pd
@@ -6,10 +7,9 @@
 
 
 class VaccineTestCase(unittest.TestCase):
-    pytest.mark.timeout(5)
-
+    @pytest.mark.timeout(15)
+    @unittest.skipIf(os.getenv("CI"), "Forbidden on CI")
     def test_Download(self):
-        """Careful! this download can take a long time"""
         df = download_covid("BA", only_header=True)
         self.assertIsInstance(df, pd.DataFrame)
         self.assertEqual(df.shape, (10000, 42))