Renew CI and update to python3.10

.github/workflows/python-package-pypi.yml

@@ -0,0 +1,49 @@
+name: PyPI
+
+on:
+  release:
+    types: [published]
+
+permissions:
+  contents: read
+
+jobs:
+
+  release-build:
+    runs-on: ubuntu-latest
+
+    steps:
+      - uses: actions/checkout@v4
+
+      - uses: actions/setup-python@v5
+        with:
+          python-version: "3.10"
+
+      - name: install packages
+        run: pip install build twine
+      - name: build release package
+        run: python -m build
+
+      - name: upload windows dists
+        uses: actions/upload-artifact@v4
+        with:
+          name: release-dists
+          path: dist/
+
+  pypi-publish:
+    environment: publish
+    runs-on: ubuntu-latest
+    needs:
+      - release-build
+    permissions:
+      id-token: write
+
+    steps:
+      - name: Retrieve release distributions
+        uses: actions/download-artifact@v4
+        with:
+          name: release-dists
+          path: dist/
+
+      - name: Publish release distributions to PyPI
+        uses: pypa/gh-action-pypi-publish@release/v1

.github/workflows/python-package-tests.yml

@@ -0,0 +1,26 @@
+name: tests
+
+on: [push, workflow_dispatch]
+
+jobs:
+  tests:
+
+    runs-on: ubuntu-latest
+    strategy:
+      matrix:
+        python: ["3.10"]
+
+    steps:
+      - uses: actions/checkout@v4
+      - name: Setup Python
+        uses: actions/setup-python@v5
+        with:
+          python-version: ${{ matrix.python }}
+      - name: Install tox
+        run: pip install tox
+      - name: Run tox
+        run: tox
+      - name: Upload coverage reports to Codecov
+        uses: codecov/[email protected]
+        with:
+          token: ${{ secrets.CODECOV_TOKEN }}

.readthedocs.yaml

@@ -6,6 +6,6 @@ sphinx:
   configuration: docs/conf.py
 
 python:
-  version: 3.6
+  version: 3.10
   install:
     - requirements: requirements_ci.txt

CONTRIBUTING.md

@@ -103,8 +103,6 @@ resource. After initialising a new repository in an empty directory with `git in
 ```bash
 $ #if you use ssh:
 $ git remote add upstream [email protected]:tempoCollaboration/OQuPy.git
-$ #if you use https
-$ git remote add upstream https://github.com/tempoCollaboration/OQuPy.git
 
 $ git fetch upstream
 $ git checkout main
@@ -121,7 +119,7 @@ $ git push origin main
 ```
 
 ### 4. Setup your local environment
-As a development environment you will need `git`, `python3.6`, `pip3` and `tox`
+As a development environment you will need `git`, `python3.10`, `pip3` and `tox`
 installed.
 
 You need `git` to
@@ -130,7 +128,7 @@ changes to the repository, while `tox` allows you to run tests on the package
 in an virtual environment (to avoid that the result of the tests depends on the
 local setup). If you are unfamiliar with `git`,
 [this](https://swcarpentry.github.io/git-novice/) is a good place to start
-learning about it. Currently the code is tested against `python3.6`, which makes it
+learning about it. Currently the code is tested against `python3.10`, which makes it
 necessary to have this version of the python interpreter installed in the
 development environment.
 
@@ -176,8 +174,6 @@ added to the project, namely:
 
 * execute the tests that check the functionality of the package (with `pytest`)
 * test the coding style (with `pylint`)
-* check that the documentation can be generated (with `sphinx`)
-
 
 #### 7.1 test all
 You can run all three tests by simply running `tox` in your local clone of the repository:
@@ -187,20 +183,19 @@ $ tox
 This performs a bunch of tests. If they all pass, it will finish with something
 like:
 ```bash
-  py36: commands succeeded
-  style: commands succeeded
-  docs: commands succeeded
-  congratulations :)
+  pytest: OK (136.95=setup[30.37]+cmd[106.58] seconds)
+  pylint: OK (51.52=setup[25.93]+cmd[25.59] seconds)
+  congratulations :) (188.56 seconds)
 ```
 
 #### 7.2 test pytest only
-You can run the pytests on python3.6 with:
+You can run the pytests on python3.10 with:
 ```bash
-$ tox -e py36
+$ tox -e pytest
 ```
 or you can pick a specific test in `./tests` to run with:
 ```bash
-$ tox -e py36 coverage/api_test.py
+$ tox -e pytest coverage/api_test.py
 ```
 Here `coverage/api_test.py` is the path of the test file *relative to the tests
 directory* and the command must be run from the *base directory of the repository.*
@@ -209,18 +204,20 @@ directory* and the command must be run from the *base directory of the repositor
 This checks the code [code style](https://www.python.org/dev/peps/pep-0008/)
 with pylint:
 ```bash
-$ tox -e style
+$ tox -e pylint
 ```
 or you can check the style of a specific file in `./oqupy` with:
 ```bash
-$ tox -e style base_api.py
+$ tox -e pylint base_api.py
 ```
 where `base_api.py` is the path of the file *relative to the oqupy
 directory* and again this command must be run from the base directory 
 of the repository.
-[comment]: # (The reason for this is that tox prepends the path you pass as an argument with './oqupy/' when using the style command, and './tests/' when using the py36 command)
+[comment]: # (The reason for this is that tox prepends the path you pass as an
+argument with './oqupy/' when using the style command, and './tests/' when 
+using the py36 command)
 
-#### 7.4 test sphinx only
+#### 7.4 build the documentation
 This invokes a sphinx-build to build the HTML documentation
 ```bash
 $ tox -e docs

PULL_REQUEST_TEMPLATE.md

@@ -2,7 +2,7 @@
 
 This checklist serves as a guide for contributors and maintainers to assess
 whether a contribution can be merged into the main branch and thus serves
-to guarantee the quality of the package. Please also read the
+to guarantee the quality of the package. Please read the
 [contribution guideline](https://github.com/tempoCollaboration/OQuPy/blob/main/CONTRIBUTING.md).
 
 Before you submit a pull request, please go through this checklist once
@@ -18,13 +18,10 @@ type of your contribution.
 * [ ] The automated test are all positive:
   - [ ] `tox -e py36` (to run `pytest`) the code tests.
   - [ ] `tox -e style` (to run `pylint`) the [code style](https://www.python.org/dev/peps/pep-0008/) tests.
-  - [ ] `tox -e docs` (to run `sphinx`) generate the documentation.
 * [ ] Added test for changed/added code.
-* [ ] API code contributions include input checks (defensive code).
-* [ ] API code contributions include helpful error messages.
 * [ ] The documentation has been updated:
   - [ ] docstring for all new functions/methods/classes/modules.
   - [ ] consistent style of all docstrings.
   - [ ] for new modules: `/docs/pages/modules.rst` has been updated.
-  - [ ] for api contributions: `/docs/pages/api.rst` has been updated.
-  - [ ] for api contributions: tutorials and examples have been updated.
+  - [ ] for new functionality: `/docs/pages/api.rst` has been updated.
+  - [ ] for new functionality: tutorials and examples have been updated.

oqupy/backends/node_array.py

@@ -112,7 +112,7 @@ def __str__(self) -> Text:
 
     def get_verbose_string(self):
         """Returns a verbose desciption of the NodeArray. """
-        ret = [self.__str__()]
+        ret = [str(self)]
         ret.append("\n")
         ret.append(f" rank = {self.rank}\n")
         ret.append(f" len = {len(self)}\n")

oqupy/helpers.py

@@ -41,7 +41,7 @@ def plot_correlations_with_parameters(
     if parameters.add_correlation_time is None:
         add_time = 0.0
         infinity = False
-    elif parameters.add_correlation_time == np.infty:
+    elif parameters.add_correlation_time == np.inf:
         add_time = 0.0
         infinity = True
     else:

oqupy/system_dynamics.py

@@ -16,6 +16,7 @@
 """
 
 from typing import List, Optional, Text, Tuple, Union
+import warnings
 
 from itertools import product
 import numpy as np
@@ -862,12 +863,12 @@ def compute_correlations_nt(
         dt_ = process_tensor.dt
     else:
         if (process_tensor.dt is not None) and (process_tensor.dt != dt):
-            UserWarning("Specified time step `dt` does not match `dt` " \
+            warnings.warn("Specified time step `dt` does not match `dt` " \
                 + "stored in the given process tensor " \
                 + f"({dt}!={process_tensor.dt}). " \
                 + "Using specified `dt`. " \
                 + "Don't specify `dt` to use the time step stored in the " \
-                + "process tensor.")
+                + "process tensor.", UserWarning)
         dt_ = dt
 
     #Check that lengths of the ops_order, ops_times and dip_ops lists are equal
@@ -892,7 +893,7 @@ def compute_correlations_nt(
 
     ret_correlations = np.empty(times_length, dtype=NpDtype)
     #This array will contain all correlations
-    ret_correlations[:] = np.NaN + 1.0j*np.NaN
+    ret_correlations[:] = np.nan + 1.0j*np.nan
 
 
     parameters = {