Dependencies: Update requirements for Python 3.11 compatibility

The following dependency requirements are updated in order to provide explicit compatibility with Python 3.11: * `circus~=0.18.0` * `pyyaml~=6.0` * `myst-nb~=0.17.0` * `kiwipy~=0.7.7` * `plumpy~=0.21.2` * `pytest~=7.0` * `pytest-benchmark~=4.0` * `archive-path~=0.4.2` * `coverage~=6.0`
aiidateam · Dec 2, 2022 · 09adc18 · 09adc18
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diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -219,7 +219,7 @@ If the profile parameter is specified in a request and the REST API does not hav
 Warning: this is beta functionality.
 It is now possible to implement custom storage backends to control where all data of an AiiDA profile is stored.
 To provide a data storage plugin, one should implement the `aiida.orm.implementation.storage_backend.StorageBackend` interface.
-The default implementation provided by `aiida-core` is the `aiida.storage.psql_dos.backend.PsqlDosBackend` which uses a PostgreSQL database for the provenance graph and a [`disk-objectstore`](#https://pypi.org/project/disk-objectstore/) container for repository files.
+The default implementation provided by `aiida-core` is the `aiida.storage.psql_dos.backend.PsqlDosBackend` which uses a PostgreSQL database for the provenance graph and a [`disk-objectstore`](https://pypi.org/project/disk-objectstore/) container for repository files.
 
 Storage backend plugins should be registered in the new entry point group `aiida.storage`.
 The default storage backend `PsqlDosBackend` has the `core.psql_dos` entry point name.

diff --git a/docs/source/conf.py b/docs/source/conf.py
@@ -82,20 +82,19 @@
 ipython_mplbackend = ''
 
 myst_enable_extensions = ['colon_fence', 'deflist']
+myst_heading_anchors = 3
 nb_merge_streams = True
-nb_render_priority = {
-  'gettext': (
-            'application/vnd.jupyter.widget-view+json',
-            'application/javascript',
-            'text/html',
-            'image/svg+xml',
-            'image/png',
-            'image/jpeg',
-            'text/markdown',
-            'text/latex',
-            'text/plain',
-        )
-}
+nb_mime_priority_overrides = [
+    ('gettext', 'application/vnd.jupyter.widget-view+json', 0),
+    ('gettext', 'application/javascript', 10),
+    ('gettext', 'text/html', 20),
+    ('gettext', 'image/svg+xml', 30),
+    ('gettext', 'image/png', 40),
+    ('gettext', 'image/jpeg', 50),
+    ('gettext', 'text/markdown', 60),
+    ('gettext', 'text/latex', 70),
+    ('gettext', 'text/plain', 80),
+]
 
 # -- Options for HTML output ---------------------------------------------------
 

diff --git a/docs/source/intro/tutorial.md b/docs/source/intro/tutorial.md
@@ -231,7 +231,7 @@ It should look something like the graph shown {ref}`below <fig_calcfun_graph>`.
 ```{code-cell} ipython3
 ---
 tags: ["hide-input"]
-render:
+mystnb:
     image:
         align: center
         width: 300px
@@ -395,7 +395,7 @@ $ verdi node graph generate 7
 ```{code-cell} ipython3
 ---
 tags: ["hide-input"]
-render:
+mystnb:
     image:
         align: center
         width: 400px
@@ -576,7 +576,7 @@ $ verdi node graph generate 14
 ```{code-cell} ipython3
 ---
 tags: ["hide-input"]
-render:
+mystnb:
     image:
         align: center
         width: 400px

diff --git a/environment.yml b/environment.yml
@@ -7,9 +7,9 @@ channels:
 dependencies:
 - python~=3.8
 - alembic~=1.2
-- archive-path~=0.4.1
+- archive-path~=0.4.2
 - aio-pika~=6.6
-- circus~=0.17.1
+- circus~=0.18.0
 - click-config-file~=0.6.0
 - click-spinner~=0.1.8
 - click~=8.1
@@ -18,17 +18,17 @@ dependencies:
 - ipython~=7.20
 - jinja2~=3.0
 - jsonschema~=3.0
-- kiwipy[rmq]~=0.7.5
+- kiwipy[rmq]~=0.7.7
 - importlib-metadata~=4.3
 - importlib-resources~=5.0
 - numpy~=1.19
 - paramiko>=2.7.2,~=2.7
-- plumpy~=0.21.1
+- plumpy~=0.21.2
 - pgsu~=0.2.1
 - psutil~=5.6
 - psycopg2-binary~=2.8
 - pytz~=2021.1
-- pyyaml~=5.4
+- pyyaml~=6.0
 - requests~=2.0
 - sqlalchemy~=1.4.22
 - tabulate~=0.8.5

diff --git a/pyproject.toml b/pyproject.toml
@@ -25,9 +25,9 @@ keywords = ["aiida", "workflows"]
 requires-python = ">=3.8"
 dependencies = [
     "alembic~=1.2",
-    "archive-path~=0.4.1",
+    "archive-path~=0.4.2",
     "aio-pika~=6.6",
-    "circus~=0.17.1",
+    "circus~=0.18.0",
     "click-config-file~=0.6.0",
     "click-spinner~=0.1.8",
     "click~=8.1",
@@ -36,17 +36,17 @@ dependencies = [
     "ipython~=7.20",
     "jinja2~=3.0",
     "jsonschema~=3.0",
-    "kiwipy[rmq]~=0.7.5",
+    "kiwipy[rmq]~=0.7.7",
     "importlib-metadata~=4.3",
     "importlib-resources~=5.0;python_version<'3.9'",
     "numpy~=1.19",
     "paramiko~=2.7,>=2.7.2",
-    "plumpy~=0.21.1",
+    "plumpy~=0.21.2",
     "pgsu~=0.2.1",
     "psutil~=5.6",
     "psycopg2-binary~=2.8",
     "pytz~=2021.1",
-    "pyyaml~=5.4",
+    "pyyaml~=6.0",
     "requests~=2.0",
     "sqlalchemy~=1.4.22",
     "tabulate~=0.8.5",
@@ -84,7 +84,7 @@ docs = [
     "sphinxext-rediraffe~=0.2.4",
     "sphinx-sqlalchemy~=0.1.1",
     "sphinx-intl[transifex]~=2.0.1",
-    "myst-nb~=0.13.2"
+    "myst-nb~=0.17.0",
 ]
 atomic_tools = [
     "PyCifRW~=4.4",
@@ -114,15 +114,15 @@ tests = [
     "aiida-export-migration-tests==0.9.0",
     "pg8000~=1.13",
     "pgtest~=1.3,>=1.3.1",
-    "pytest~=6.2",
+    "pytest~=7.0",
     "pytest-asyncio~=0.12,<0.17",
     "pytest-timeout~=1.3",
     "pytest-cov~=2.7,<2.11",
     "pytest-rerunfailures~=9.1,>=9.1.1",
-    "pytest-benchmark~=3.2",
+    "pytest-benchmark~=4.0",
     "pytest-regressions~=2.2",
     "pympler~=0.9",
-    "coverage<5.0",
+    "coverage~=6.0",
     "sqlalchemy-utils~=0.37.2",
     "sphinx~=4.0",
     "docutils==0.16",
@@ -314,7 +314,7 @@ docstring-min-length = 5
 max-locals = 20
 
 [tool.pytest.ini_options]
-minversion = "6.0"
+minversion = "7.0"
 addopts = "--benchmark-skip --durations=50 --cov-report xml --cov-append "
 testpaths = [
     "tests",

diff --git a/requirements/requirements-py-3.10.txt b/requirements/requirements-py-3.10.txt
@@ -4,7 +4,7 @@ aiormq==3.3.1
 alabaster==0.7.12
 alembic==1.7.5
 aniso8601==9.0.1
-archive-path==0.4.1
+archive-path==0.4.2
 argon2-cffi==21.1.0
 ase==3.22.0
 asn1crypto==1.4.0
@@ -18,12 +18,12 @@ bleach==4.1.0
 certifi==2021.10.8
 cffi==1.15.0
 charset-normalizer==2.0.8
-circus==0.17.1
+circus==0.18.0
 click==8.1.0
 click-config-file==0.6.0
 click-spinner==0.1.10
 configobj==5.0.6
-coverage==4.5.4
+coverage==6.5.0
 cryptography==36.0.0
 cycler==0.11.0
 debugpy==1.5.1
@@ -58,7 +58,7 @@ jupyter-console==6.4.0
 jupyter-core==4.11.2
 jupyterlab-pygments==0.1.2
 jupyterlab-widgets==1.0.2
-kiwipy==0.7.5
+kiwipy==0.7.7
 kiwisolver==1.3.2
 Mako==1.2.2
 MarkupSafe==2.0.1
@@ -68,7 +68,7 @@ mistune==0.8.4
 monty==2021.8.17
 mpmath==1.2.1
 multidict==5.2.0
-myst-nb==0.13.2
+myst-nb==0.17.1
 nbclient==0.5.9
 nbconvert==6.3.0
 nbformat==5.1.3
@@ -90,7 +90,7 @@ pickleshare==0.7.5
 Pillow==9.3.0
 plotly==5.4.0
 pluggy==1.0.0
-plumpy==0.21.1
+plumpy==0.21.2
 prometheus-client==0.12.0
 prompt-toolkit==3.0.23
 psutil==5.8.0
@@ -108,9 +108,9 @@ PyMySQL==0.9.3
 PyNaCl==1.4.0
 pyparsing==2.4.7
 pyrsistent==0.18.0
-pytest==6.2.5
+pytest==7.2.0
 pytest-asyncio==0.16.0
-pytest-benchmark==3.4.1
+pytest-benchmark==4.0.0
 pytest-cov==2.10.1
 pytest-datadir==1.3.1
 pytest-regressions==2.2.0
@@ -119,7 +119,7 @@ pytest-timeout==1.4.2
 python-memcached==1.59
 pytray==0.3.2
 pytz==2021.3
-PyYAML==5.4.1
+PyYAML==6.0.0
 pyzmq==22.3.0
 qtconsole==5.2.1
 QtPy==1.11.2

diff --git a/requirements/requirements-py-3.8.txt b/requirements/requirements-py-3.8.txt
@@ -4,7 +4,7 @@ aiormq==3.3.1
 alabaster==0.7.12
 alembic==1.7.5
 aniso8601==9.0.1
-archive-path==0.4.1
+archive-path==0.4.2
 argon2-cffi==21.1.0
 ase==3.22.0
 asn1crypto==1.4.0
@@ -18,12 +18,12 @@ bleach==4.1.0
 certifi==2021.10.8
 cffi==1.15.0
 charset-normalizer==2.0.8
-circus==0.17.1
+circus==0.18.0
 click==8.1.0
 click-config-file==0.6.0
 click-spinner==0.1.10
 configobj==5.0.6
-coverage==4.5.4
+coverage==6.5.0
 cryptography==36.0.0
 cycler==0.11.0
 debugpy==1.5.1
@@ -59,7 +59,7 @@ jupyter-console==6.4.0
 jupyter-core==4.11.2
 jupyterlab-pygments==0.1.2
 jupyterlab-widgets==1.0.2
-kiwipy==0.7.5
+kiwipy==0.7.7
 kiwisolver==1.3.2
 Mako==1.2.2
 MarkupSafe==2.0.1
@@ -69,7 +69,7 @@ mistune==0.8.4
 monty==2021.8.17
 mpmath==1.2.1
 multidict==5.2.0
-myst-nb==0.13.2
+myst-nb==0.17.1
 nbclient==0.5.9
 nbconvert==6.3.0
 nbformat==5.1.3
@@ -91,7 +91,7 @@ pickleshare==0.7.5
 Pillow==9.3.0
 plotly==5.4.0
 pluggy==1.0.0
-plumpy==0.21.1
+plumpy==0.21.2
 prometheus-client==0.12.0
 prompt-toolkit==3.0.23
 psutil==5.8.0
@@ -109,9 +109,9 @@ PyMySQL==0.9.3
 PyNaCl==1.4.0
 pyparsing==2.4.7
 pyrsistent==0.18.0
-pytest==6.2.5
+pytest==7.2.0
 pytest-asyncio==0.16.0
-pytest-benchmark==3.4.1
+pytest-benchmark==4.0.0
 pytest-cov==2.10.1
 pytest-datadir==1.3.1
 pytest-regressions==2.2.0
@@ -120,7 +120,7 @@ pytest-timeout==1.4.2
 python-memcached==1.59
 pytray==0.3.2
 pytz==2021.3
-PyYAML==5.4.1
+PyYAML==6.0.0
 pyzmq==22.3.0
 qtconsole==5.2.1
 QtPy==1.11.2

diff --git a/requirements/requirements-py-3.9.txt b/requirements/requirements-py-3.9.txt
@@ -4,7 +4,7 @@ aiormq==3.3.1
 alabaster==0.7.12
 alembic==1.7.5
 aniso8601==9.0.1
-archive-path==0.4.1
+archive-path==0.4.2
 argon2-cffi==21.1.0
 ase==3.22.0
 asn1crypto==1.4.0
@@ -18,12 +18,12 @@ bleach==4.1.0
 certifi==2021.10.8
 cffi==1.15.0
 charset-normalizer==2.0.8
-circus==0.17.1
+circus==0.18.0
 click==8.1.0
 click-config-file==0.6.0
 click-spinner==0.1.10
 configobj==5.0.6
-coverage==4.5.4
+coverage==6.5.0
 cryptography==36.0.0
 cycler==0.11.0
 debugpy==1.5.1
@@ -58,7 +58,7 @@ jupyter-console==6.4.0
 jupyter-core==4.11.2
 jupyterlab-pygments==0.1.2
 jupyterlab-widgets==1.0.2
-kiwipy==0.7.5
+kiwipy==0.7.7
 kiwisolver==1.3.2
 Mako==1.2.2
 MarkupSafe==2.0.1
@@ -68,7 +68,7 @@ mistune==0.8.4
 monty==2021.8.17
 mpmath==1.2.1
 multidict==5.2.0
-myst-nb==0.13.2
+myst-nb==0.17.1
 nbclient==0.5.9
 nbconvert==6.3.0
 nbformat==5.1.3
@@ -90,7 +90,7 @@ pickleshare==0.7.5
 Pillow==9.3.0
 plotly==5.4.0
 pluggy==1.0.0
-plumpy==0.21.1
+plumpy==0.21.2
 prometheus-client==0.12.0
 prompt-toolkit==3.0.23
 psutil==5.8.0
@@ -108,9 +108,9 @@ PyMySQL==0.9.3
 PyNaCl==1.4.0
 pyparsing==2.4.7
 pyrsistent==0.18.0
-pytest==6.2.5
+pytest==7.2.0
 pytest-asyncio==0.16.0
-pytest-benchmark==3.4.1
+pytest-benchmark==4.0.0
 pytest-cov==2.10.1
 pytest-datadir==1.3.1
 pytest-regressions==2.2.0
@@ -119,7 +119,7 @@ pytest-timeout==1.4.2
 python-memcached==1.59
 pytray==0.3.2
 pytz==2021.3
-PyYAML==5.4.1
+PyYAML==6.0.0
 pyzmq==22.3.0
 qtconsole==5.2.1
 QtPy==1.11.2