Merge branch 'dev' into samukweku/summarise

.darglint

@@ -1,4 +1,4 @@
 [darglint]
-docstring_style=sphinx
+docstring_style=google
 strictness=short
 ignore_regex=^(test_|_)(.*)

.requirements/all.txt

@@ -1,9 +1,11 @@
 #
-# This file is autogenerated by pip-compile with python 3.9
-# To update, run:
+# This file is autogenerated by pip-compile with Python 3.9
+# by the following command:
 #
 #    pip-compile .requirements/all.in
 #
+appnope==0.1.3
+    # via ipython
 asttokens==2.0.5
     # via stack-data
 attrs==21.4.0
@@ -15,9 +17,9 @@ attrs==21.4.0
 backcall==0.2.0
     # via ipython
 biopython==1.79
-    # via -r biology.in
+    # via -r .requirements/biology.in
 black==22.1.0
-    # via -r dev.in
+    # via -r .requirements/dev.in
 cfgv==3.3.1
     # via pre-commit
 click==8.0.4
@@ -27,11 +29,13 @@ click==8.0.4
     #   mkdocs
     #   pip-tools
 colorama==0.4.4
-    # via interrogate
+    # via
+    #   griffe
+    #   interrogate
 coverage[toml]==6.3.2
     # via pytest-cov
 darglint==1.8.1
-    # via -r dev.in
+    # via -r .requirements/dev.in
 decorator==5.1.1
     # via ipython
 distlib==0.3.4
@@ -44,31 +48,37 @@ filelock==3.6.0
     # via virtualenv
 flake8==4.0.1
     # via
-    #   -r dev.in
+    #   -r .requirements/dev.in
     #   pandas-vet
 ghp-import==2.0.2
     # via mkdocs
+griffe==0.25.4
+    # via mkdocstrings-python
 hypothesis==6.39.3
-    # via -r testing.in
+    # via -r .requirements/testing.in
 identify==2.4.11
     # via pre-commit
 importlib-metadata==4.11.2
-    # via mkdocs
+    # via
+    #   markdown
+    #   mkdocs
 iniconfig==1.1.1
     # via pytest
 interrogate==1.5.0
-    # via -r testing.in
+    # via -r .requirements/testing.in
 ipython==8.1.1
-    # via -r docs.in
+    # via -r .requirements/docs.in
 isort==5.10.1
-    # via -r dev.in
+    # via -r .requirements/dev.in
 jedi==0.18.1
     # via ipython
 jinja2==3.0.3
     # via
     #   mkdocs
     #   mkdocs-material
     #   mkdocstrings
+lazy-loader==0.1
+    # via -r .requirements/base.in
 markdown==3.3.6
     # via
     #   mkdocs
@@ -88,26 +98,30 @@ mergedeep==1.3.4
     # via mkdocs
 mkdocs==1.2.3
     # via
-    #   -r docs.in
+    #   -r .requirements/docs.in
     #   mkdocs-autorefs
     #   mkdocs-material
     #   mkdocstrings
 mkdocs-autorefs==0.4.1
     # via mkdocstrings
 mkdocs-material==8.2.5
-    # via -r docs.in
+    # via -r .requirements/docs.in
 mkdocs-material-extensions==1.0.3
     # via mkdocs-material
-mkdocstrings==0.17.0
-    # via -r docs.in
+mkdocstrings==0.20.0
+    # via
+    #   -r .requirements/docs.in
+    #   mkdocstrings-python
+mkdocstrings-python==0.8.3
+    # via -r .requirements/docs.in
 mpmath==1.2.1
     # via sympy
 multipledispatch==0.6.0
-    # via -r base.in
+    # via -r .requirements/base.in
 mypy-extensions==0.4.3
     # via black
 natsort==8.1.0
-    # via -r base.in
+    # via -r .requirements/base.in
 nodeenv==1.6.0
     # via pre-commit
 numpy==1.22.3
@@ -127,9 +141,9 @@ pandas==1.4.1
     #   pandas-flavor
     #   xarray
 pandas-flavor==0.2.0
-    # via -r base.in
+    # via -r .requirements/base.in
 pandas-vet==0.2.3
-    # via -r testing.in
+    # via -r .requirements/testing.in
 parso==0.8.3
     # via jedi
 pathspec==0.9.0
@@ -141,15 +155,15 @@ pexpect==4.8.0
 pickleshare==0.7.5
     # via ipython
 pip-tools==6.5.1
-    # via -r dev.in
+    # via -r .requirements/dev.in
 platformdirs==2.5.1
     # via
     #   black
     #   virtualenv
 pluggy==1.0.0
     # via pytest
 pre-commit==2.17.0
-    # via -r dev.in
+    # via -r .requirements/dev.in
 prompt-toolkit==3.0.28
     # via ipython
 ptyprocess==0.7.0
@@ -158,7 +172,7 @@ pure-eval==0.2.2
     # via stack-data
 py==1.11.0
     # via
-    #   -r testing.in
+    #   -r .requirements/testing.in
     #   interrogate
     #   pytest
     #   pytest-forked
@@ -179,25 +193,23 @@ pymdown-extensions==9.2
 pyparsing==3.0.7
     # via packaging
 pyspark==3.2.2
-    # via -r spark.in
+    # via -r .requirements/spark.in
 pytest==7.0.1
     # via
-    #   -r testing.in
+    #   -r .requirements/testing.in
     #   pytest-cov
     #   pytest-forked
     #   pytest-xdist
 pytest-cov==3.0.0
-    # via -r testing.in
+    # via -r .requirements/testing.in
 pytest-forked==1.4.0
     # via pytest-xdist
 pytest-xdist==2.5.0
-    # via -r testing.in
+    # via -r .requirements/testing.in
 python-dateutil==2.8.2
     # via
     #   ghp-import
     #   pandas
-pytkdocs==0.16.1
-    # via mkdocstrings
 pytz==2021.3
     # via pandas
 pyyaml==6.0
@@ -208,7 +220,7 @@ pyyaml==6.0
 pyyaml-env-tag==0.1
     # via mkdocs
 scipy==1.8.0
-    # via -r base.in
+    # via -r .requirements/base.in
 six==1.16.0
     # via
     #   asttokens
@@ -234,13 +246,15 @@ tomli==2.0.1
     #   pep517
     #   pytest
 tqdm==4.63.0
-    # via -r chemistry.in
+    # via -r .requirements/chemistry.in
 traitlets==5.1.1
     # via
     #   ipython
     #   matplotlib-inline
+typing-extensions==4.4.0
+    # via black
 unyt==2.8.0
-    # via -r engineering.in
+    # via -r .requirements/engineering.in
 virtualenv==20.13.3
     # via pre-commit
 watchdog==2.1.6

.requirements/docs.in

@@ -1,6 +1,7 @@
 mkdocs
 mkdocs-material
-mkdocstrings<0.18
+mkdocstrings>=0.19.0
+mkdocstrings-python
 ipython>7.31.1
 -r biology.in
 -r chemistry.in