Update upstream packages

* Use docs-versions-menu instead of doctr-versions-menu * Use Python 3.8 as main development version * Use latest QuTiP, Scipy, and Numpy packages * Drop support for Python 3.5
qucontrol · May 28, 2021 · cfe6b10 · cfe6b10
1 parent c9e7883
commit cfe6b10
Show file tree

Hide file tree

Showing 9 changed files with 81 additions and 96 deletions.
diff --git a/.github/workflows/docs.yml b/.github/workflows/docs.yml
@@ -12,9 +12,9 @@ jobs:
       - uses: actions/checkout@v2
 
       - uses: actions/setup-python@v2
-        name: Install Python 3.7
+        name: Install Python 3.8
         with:
-          python-version: 3.7
+          python-version: 3.8
 
       - name: Install apt packages
         run: sudo apt-get install graphviz imagemagick pandoc pandoc-citeproc
@@ -50,12 +50,12 @@ jobs:
     steps:
 
       - uses: actions/setup-python@v2
-        name: Install Python 3.7
+        name: Install Python 3.8
         with:
-          python-version: 3.7
+          python-version: 3.8
 
       - name: Install deploy requirements
-        run: pip install git+https://github.com/goerz/doctr_versions_menu.git@master#egg=doctr_versions_menu
+        run: pip install docs-versions-menu
 
       - name: Get branch name
         shell: bash
@@ -96,8 +96,8 @@ jobs:
         shell: bash
         run: rm -rf _krotov_docs
 
-      - name: Run doctr-versions-menu
-        run: doctr-versions-menu
+      - name: Run docs-versions-menu
+        run: docs-versions-menu
 
       - name: Get the previous commit message
         id: get_previous_commit

diff --git a/.github/workflows/test.yml b/.github/workflows/test.yml
@@ -17,15 +17,15 @@ jobs:
         include:
           - title: Codestyle and Main Tests
             os: ubuntu-18.04
-            python: 3.7
+            python: 3.8
             commands: |
               $tox -e run-blackcheck,run-isortcheck
-              $tox -e py37-test -- $default_tests
+              $tox -e py38-test -- $default_tests
             coverage: true
           - title: Oldest supported Python
             os: ubuntu-18.04
-            python: 3.5
-            commands: $tox -e py35-test -- $default_tests
+            python: 3.6
+            commands: $tox -e py36-test -- $default_tests
             coverage: false
           - title: QuTiP master
             os: ubuntu-18.04
@@ -40,53 +40,53 @@ jobs:
             coverage: false
           - title: MacOS
             os: macos-latest
-            python: 3.7
-            commands: $tox -e py37-test -- $default_tests  docs/notebooks/01_example_simple_state_to_state.ipynb
+            python: 3.8
+            commands: $tox -e py38-test -- $default_tests  docs/notebooks/01_example_simple_state_to_state.ipynb
             coverage: true
           - title: Notebook 1 (State-to-State)
             os: ubuntu-18.04
-            python: 3.7
-            commands: $tox -e py37-test -- docs/notebooks/01_example_simple_state_to_state.ipynb
+            python: 3.8
+            commands: $tox -e py38-test -- docs/notebooks/01_example_simple_state_to_state.ipynb
             coverage: true
           - title: Notebook 2 (RWA)
             os: ubuntu-18.04
-            python: 3.7
-            commands: $tox -e py37-test -- docs/notebooks/02_example_lambda_system_rwa_complex_pulse.ipynb
+            python: 3.8
+            commands: $tox -e py38-test -- docs/notebooks/02_example_lambda_system_rwa_complex_pulse.ipynb
             coverage: true
           - title: Notebook 3 (Non-Hermitian)
             os: ubuntu-18.04
-            python: 3.7
-            commands: $tox -e py37-test -- docs/notebooks/03_example_lambda_system_rwa_non_hermitian.ipynb
+            python: 3.8
+            commands: $tox -e py38-test -- docs/notebooks/03_example_lambda_system_rwa_non_hermitian.ipynb
             coverage: true
           - title: Notebook 4 (Density Matrix)
             os: ubuntu-18.04
-            python: 3.7
-            commands: $tox -e py37-test -- docs/notebooks/04_example_dissipative_qubit_reset.ipynb
+            python: 3.8
+            commands: $tox -e py38-test -- docs/notebooks/04_example_dissipative_qubit_reset.ipynb
             coverage: true
           - title: Notebook 5 (Quantum Gate)
             os: ubuntu-18.04
-            python: 3.7
-            commands: $tox -e py37-test -- docs/notebooks/05_example_transmon_xgate.ipynb
+            python: 3.8
+            commands: $tox -e py38-test -- docs/notebooks/05_example_transmon_xgate.ipynb
             coverage: true
           - title: Notebook 6 (3 States)
             os: ubuntu-18.04
-            python: 3.7
-            commands: $tox -e py37-test -- docs/notebooks/06_example_3states.ipynb
+            python: 3.8
+            commands: $tox -e py38-test -- docs/notebooks/06_example_3states.ipynb
             coverage: true
           - title: Notebook 7 (Perfect Entanglers)
             os: ubuntu-18.04
-            python: 3.7
-            commands: $tox -e py37-test -- docs/notebooks/07_example_PE.ipynb
+            python: 3.8
+            commands: $tox -e py38-test -- docs/notebooks/07_example_PE.ipynb
             coverage: true
           - title: Notebook 8 (Ensemble Optimization)
             os: ubuntu-18.04
-            python: 3.7
-            commands: $tox -e py37-test -- docs/notebooks/08_example_ensemble.ipynb
+            python: 3.8
+            commands: $tox -e py38-test -- docs/notebooks/08_example_ensemble.ipynb
             coverage: true
           - title: Notebook 9 (NumPy)
             os: ubuntu-18.04
-            python: 3.7
-            commands: $tox -e py37-test -- docs/notebooks/09_example_numpy.ipynb
+            python: 3.8
+            commands: $tox -e py38-test -- docs/notebooks/09_example_numpy.ipynb
             coverage: true
     steps:
       - uses: actions/checkout@v2

diff --git a/CONTRIBUTING.rst b/CONTRIBUTING.rst
@@ -116,7 +116,7 @@ If you are a member of the `qucontrol organization`_, there is no need to fork
 Development Prerequisites
 -------------------------
 
-Contributing to the package's developments requires that you have Python 3.7
+Contributing to the package's developments requires that you have Python 3.8
 and tox_ installed. It is strongly recommended that you also have installations
 of all other supported Python versions. The recommended way to install multiple
 versions of Python at the same time is through pyenv_ (or pyenv-win_ on
@@ -136,7 +136,7 @@ that you may run into occasional binary incompatibilities between conda packages
    If you want to use `conda`, you must use the ``tox-conda.ini`` configuration
    file. That is, run all ``make`` comands as e.g.
    ``make TOXINI=tox-conda.ini test`` and ``tox`` commands as e.g.
-   ``tox -c tox-conda.ini -e py35-test,py36-test,py37-test``. Alternatively,
+   ``tox -c tox-conda.ini -e py38-test``. Alternatively,
    make ``tox-conda.ini`` the default by copying it to ``tox.ini``.
 
 .. _pyenv: https://github.com/pyenv/pyenv
@@ -264,7 +264,7 @@ to run the entire test suite, or
 
 .. code-block:: shell
 
-    tox -e py35-test,py36-test,py37-test
+    tox -e py38-test
 
 if ``make`` is not available.
 
@@ -278,7 +278,7 @@ the `nbval plugin`_.
 
 .. _test coverage: https://codecov.io/gh/qucontrol/krotov
 .. _pytest: https://docs.pytest.org/en/latest/
-.. _doctests: https://docs.python.org/3.7/library/doctest.html
+.. _doctests: https://docs.python.org/3.8/library/doctest.html
 .. _pytest doctest plugin: https://docs.pytest.org/en/latest/doctest.html
 .. _nbval plugin: https://nbval.readthedocs.io/en/latest/
 
@@ -680,11 +680,11 @@ To run e.g. only the tests defined in ``tests/test_krotov.py``, use any of the f
 
     make test TESTS=tests/test_krotov.py
 
-    tox -e py37-test -- tests/test_krotov.py
+    tox -e py38-test -- tests/test_krotov.py
 
     tox -e run-cmd -- pytest tests/test_krotov.py
 
-    .tox/py37/bin/pytest tests/test_krotov.py
+    .tox/py38/bin/pytest tests/test_krotov.py
 
 See the `pytest test selection docs`_ for details.
 

diff --git a/Makefile b/Makefile
@@ -54,10 +54,7 @@ pylint-check: bootstrap ## check style with pylint
 	$(TOX) -e run-pylint
 
 test: bootstrap ## run tests for current stable Python release
-	$(TOX) -e py37-test -- $(TESTS)
-
-test35: bootstrap ## run tests for Python 3.5
-	$(TOX) -e py35-test -- $(TESTS)
+	$(TOX) -e py38-test -- $(TESTS)
 
 test36: bootstrap ## run tests for Python 3.6
 	$(TOX) -e py36-test -- $(TESTS)
@@ -101,7 +98,7 @@ isort-check: bootstrap ## Check all src and test files for correctly sorted impo
 isort: bootstrap ## Sort imports in all src and test files
 	$(TOX) -e run-isort
 
-coverage: test37  ## generate coverage report in ./htmlcov
+coverage: test38  ## generate coverage report in ./htmlcov
 	$(TOX) -e coverage
 	@echo "open htmlcov/index.html"
 

diff --git a/docs/conf.py b/docs/conf.py
@@ -67,7 +67,7 @@ def generate_patched_readme(_):
 nitpick_ignore = [("py:class", "callable")]
 
 extensions = [
-    "doctr_versions_menu",
+    "docs_versions_menu",
     "nbsphinx",
     "sphinx.ext.autodoc",
     "sphinx.ext.autosummary",
@@ -506,7 +506,7 @@ def iad_add_directive_header(self, sig):
 # This is the file name suffix for HTML files (e.g. ".xhtml").
 # html_file_suffix = None
 
-doctr_versions_menu_conf = {'menu_title': 'Docs'}
+docs_versions_menu_conf = {'menu_title': 'Docs'}
 
 # -- Options for nbsphinx -0---------------------------------------------------
 

diff --git a/setup.cfg b/setup.cfg
@@ -1,6 +1,3 @@
-[bdist_wheel]
-universal = 1
-
 [flake8]
 exclude = docs
 max-line-length = 79

diff --git a/setup.py b/setup.py
@@ -38,13 +38,12 @@ def get_version(filename):
 
 # requirements for development (testing, generating docs)
 dev_requirements = [
-    'better-apidoc==0.3.1',
+    'better-apidoc==0.3.2',
     'click',
     'codecov',
     'coverage<5.0',
     # https://github.com/computationalmodelling/nbval/issues/129
-    'doctr',
-    'doctr-versions-menu',
+    'docs-versions-menu',
     'flake8',
     'gitpython',
     'isort==4.3.*',
@@ -59,7 +58,7 @@ def get_version(filename):
     'pytest',
     'pytest-cov<=2.6.1',
     'pytest-xdist',
-    'sphinx',
+    'sphinx<4.0',
     'sphinx-autobuild',
     'sphinx-copybutton',
     'sphinx_rtd_theme',
@@ -87,10 +86,10 @@ def get_version(filename):
         'Intended Audience :: Science/Research',
         'License :: OSI Approved :: BSD License',
         'Natural Language :: English',
-        'Programming Language :: Python :: 3.5',
         'Programming Language :: Python :: 3.6',
         'Programming Language :: Python :: 3.7',
         'Programming Language :: Python :: 3.8',
+        'Programming Language :: Python :: 3.9',
         'Framework :: Jupyter',
         'Natural Language :: English',
         'Operating System :: OS Independent',
@@ -100,7 +99,7 @@ def get_version(filename):
     description=(
         "Python implementation of Krotov's method for quantum optimal control"
     ),
-    python_requires='~=3.5',
+    python_requires='~=3.6',
     install_requires=requirements,
     extras_require={'dev': dev_requirements, 'extras': dev_extras},
     license="BSD license",

diff --git a/tox-conda.ini b/tox-conda.ini
@@ -1,6 +1,6 @@
 [tox]
 minversion = 3.7
-envlist = py35-{test,runcmd}, py36-{test,runcmd}, py37-{test,runcmd}, py38-{test,runcmd}, run-{cmd,blackcheck,black,isort,isortcheck}, docs, coverage
+envlist = py36-{test,runcmd}, py37-{test,runcmd}, py38-{test,runcmd}, run-{cmd,blackcheck,black,isort,isortcheck}, docs, coverage
 requires = tox-conda
 
 [testenv:.tox]
@@ -10,31 +10,27 @@ envdir = {toxworkdir}/.tox
 [testenv]
 basepython =
     # current "stable" python
-    py37,run,docs,coverage,clean,bootstrap: python3.7
+    py38,run,docs,coverage,clean,bootstrap: python3.8
     # older pythons
-    py38: python3.8
+    py37: python3.7
     py36: python3.6
-    py35: python3.5
 envdir =
     # current "stable" environment
-    py37,run,docs,coverage: {toxworkdir}/py37
+    py38,run,docs,coverage: {toxworkdir}/py38
     # other "stable" environment
-    py38: {toxworkdir}/py38
+    py37: {toxworkdir}/py37
     py36: {toxworkdir}/py36
-    py35: {toxworkdir}/py35
 conda_deps =
     cython
-    py38: numpy=1.18.1
-    py37,run,docs,coverage: numpy=1.17.2
+    py38,run,docs,coverage: numpy=1.20.3
+    py37: numpy=1.17.2
     py36: numpy=1.15.4
-    py35: numpy=1.15.2
-    py38: scipy=1.4.1
-    py37,run,docs,coverage: scipy=1.3.1
+    py38,run,docs,coverage: scipy=1.6.3
+    py37: scipy=1.3.1
     py36: scipy=1.2.0
-    py35: scipy=1.1.0
-    py38: qutip=4.5.0
-    py37,run,docs,coverage: qutip=4.5.0
-    py36,py35: qutip=4.3.1
+    py38,run,docs,coverage: qutip=4.6.1
+    py37: qutip=4.5.0
+    py36: qutip=4.3.1
 conda_channels=
     default
     conda-forge
@@ -45,15 +41,15 @@ setenv =
     MATPLOTLIBRC = tests
 passenv = HOME CI TRAVIS TRAVIS_* COVERALLS* CODECOV* SPELLCHECK SSH_AUTH_SOCK http_proxy https_proxy no_proxy
 description =
-    py{35,36,37,38}-test: Run tests in the corresponding environment
-    py{35,36,37,38}-runcmd: Run arbitrary command following "--" in the corresponding environment
+    py{36,37,38}-test: Run tests in the corresponding environment
+    py{36,37,38}-runcmd: Run arbitrary command following "--" in the corresponding environment
     py38qtm-test: Run tests with Python 3.8 and the QuTiP-master
     py38qtm-runcmd: Run arbitrary command following "--" in the environment for py38qtm-test
 commands_pre =
     python -V
 commands =
-    py{35,36,37,38}-runcmd: {posargs:python -c 'print("No command")'}
-    py{35,36,37,38}-test: py.test -vvv --doctest-modules --cov=krotov --nbval --sanitize-with docs/nbval_sanitize.cfg --ignore docs/_build/ --durations=10 -x -s {posargs:src tests docs README.rst}
+    py{36,37,38}-runcmd: {posargs:python -c 'print("No command")'}
+    py{36,37,38}-test: py.test -vvv --doctest-modules --cov=krotov --nbval --sanitize-with docs/nbval_sanitize.cfg --ignore docs/_build/ --durations=10 -x -s {posargs:src tests docs README.rst}
 
 
 [testenv:docs]
@@ -147,7 +143,7 @@ commands =
 
 [testenv:coverage]
 description = Generate a coverage report
-depends = py37-test
+depends = py38-test
 commands =
     coverage html
     python -c 'import pathlib; print("coverage report available in \{\}".format(pathlib.Path(".") / "htmlcov" / "index.html"))'