MAINT: update minimum required versions and CI maintanance (#199)

* CI: update minimum versions following SPEC0 as of Q4 2023

* CI: adding python 3.12 to testing

* MAINT: use the scientific python extra pip index for dev wheels

Keep reinstalling numpy with a separated pip command to ensure the dev version is picked up even if a downstream dependency upper limited it

* MAINT: content fixes for numpy 2.0

Author: bsipocz

.github/workflows/ci_tests_run_notebooks.yml

@@ -31,14 +31,19 @@ jobs:
             os: ubuntu-latest
 
           - python-version: '3.11'
-            toxenv: py311-test-devdeps
-            name: with Python 3.11 and developer versioned dependencies
+            toxenv: py311-test
+            name: with Python 3.11 and latest released version of dependencies
+            os: ubuntu-latest
+
+          - python-version: '3.12'
+            toxenv: py312-test-devdeps
+            name: with Python 3.12 and developer versioned dependencies
             os: ubuntu-latest
 
     steps:
-    - uses: actions/checkout@v3
+    - uses: actions/checkout@v4
     - name: Set up Python ${{ matrix.python-version }}
-      uses: actions/setup-python@v4
+      uses: actions/setup-python@v5
       with:
         python-version: ${{ matrix.python-version }}
 

content/tutorial-ma.md

@@ -92,7 +92,7 @@ rows of this file, since they contain other data we are not interested in. Separ
 # Read just the dates for columns 4-18 from the first row
 dates = np.genfromtxt(
     filename,
-    dtype=np.unicode_,
+    dtype=np.str_,
     delimiter=",",
     max_rows=1,
     usecols=range(4, 18),
@@ -102,7 +102,7 @@ dates = np.genfromtxt(
 # columns, skipping the first six rows
 locations = np.genfromtxt(
     filename,
-    dtype=np.unicode_,
+    dtype=np.str_,
     delimiter=",",
     skip_header=6,
     usecols=(0, 1),
@@ -119,7 +119,7 @@ nbcases = np.genfromtxt(
 )
 ```
 
-Included in the `numpy.genfromtxt` function call, we have selected the [numpy.dtype](https://numpy.org/devdocs/reference/generated/numpy.dtype.html#numpy.dtype) for each subset of the data (either an integer - `numpy.int_` - or a string of characters - `numpy.unicode_`). We have also used the `encoding` argument to select `utf-8-sig` as the encoding for the file (read more about encoding in the [official Python documentation](https://docs.python.org/3/library/codecs.html#encodings-and-unicode). You can read more about the `numpy.genfromtxt` function from the [Reference Documentation](https://numpy.org/devdocs/reference/generated/numpy.genfromtxt.html#numpy.genfromtxt) or from the [Basic IO tutorial](https://numpy.org/devdocs/user/basics.io.genfromtxt.html).
+Included in the `numpy.genfromtxt` function call, we have selected the [numpy.dtype](https://numpy.org/devdocs/reference/generated/numpy.dtype.html#numpy.dtype) for each subset of the data (either an integer - `numpy.int_` - or a string of characters - `numpy.str_`). We have also used the `encoding` argument to select `utf-8-sig` as the encoding for the file (read more about encoding in the [official Python documentation](https://docs.python.org/3/library/codecs.html#encodings-and-unicode). You can read more about the `numpy.genfromtxt` function from the [Reference Documentation](https://numpy.org/devdocs/reference/generated/numpy.genfromtxt.html#numpy.genfromtxt) or from the [Basic IO tutorial](https://numpy.org/devdocs/user/basics.io.genfromtxt.html).
 
 +++
 

tox.ini

@@ -1,32 +1,38 @@
 [tox]
 envlist =
-    py{39,310,311}-test{,-oldestdeps,-devdeps,-predeps}{,-buildhtml}
+    py{39,310,311,312}-test{,-oldestdeps,-devdeps,-predeps}{,-buildhtml}
 requires =
     pip >= 19.3.1
 
 [testenv]
 
 description = run tests
 
+setenv =
+    devdeps: PIP_EXTRA_INDEX_URL =  https://pypi.anaconda.org/scientific-python-nightly-wheels/simple
+
 deps =
     # We use these files to specify all the dependencies, and below we override
     # versions for specific testing schenarios
     -rtest_requirements.txt
     -rsite/requirements.txt
     -rrequirements.txt
 
-    oldestdeps: numpy==1.20
-    oldestdeps: matplotlib==3.4
-    oldestdeps: scipy==1.6
-    oldestdeps: pandas==1.2
+    oldestdeps: numpy==1.23
+    oldestdeps: matplotlib==3.6
+    oldestdeps: scipy==1.8
+    oldestdeps: pandas==1.4
+
+    devdeps: numpy>=0.0.dev0
+    devdeps: scipy>=0.0.dev0
+    devdeps: matplotlib>=0.0.dev0
+    devdeps: pandas>=0.0.dev0
 
 allowlist_externals = bash
 
 commands =
-    devdeps: pip install -U --pre --only-binary :all: -i https://pypi.anaconda.org/scipy-wheels-nightly/simple numpy
-    devdeps: pip install -U --pre --only-binary :all: -i https://pypi.anaconda.org/scipy-wheels-nightly/simple scipy
-    devdeps: pip install -U --pre --only-binary :all: -i https://pypi.anaconda.org/scipy-wheels-nightly/simple matplotlib
-    devdeps: pip install -U --pre --only-binary :all: -i https://pypi.anaconda.org/scipy-wheels-nightly/simple pandas
+    # Force numpy reinstall to work around upper version limits in downstream dependencies (e.g. pandas)
+    devdeps: pip install -U --pre --no-deps --extra-index-url https://pypi.anaconda.org/scientific-python-nightly-wheels/simple numpy
 
     pip freeze