Update website dataset docs (#41)

* updated dataset incl misc

* miscellaneous + todos

* updated split table to v2

* lint

* chore: update dataset.md

* update links table

* lint

* fix: add similarity metrics descriptions

* fix: add posebusters descriptions

* Apply suggestions from code review

padix-key suggestions

Co-authored-by: Patrick Kunzmann <padix.key@gmail.com>

* Update docs/dataset.md

Co-authored-by: Patrick Kunzmann <padix.key@gmail.com>

* fix: update posebusters_checks.tsv

* fix: update reformat cluster description

* fix: fix some description in docs/dataset.md

* fix: update docs/dataset.md

* fix: add description to split.yaml

* chore: update tables

* fix: MyST syntax

* chore: update tables

* highlight split.yaml

* fix: fix formating issue

* chore: small verbiage fixes

* fix: concurrency in main publishing workflow

* docs: polish docs regarding plinder.data and plinder.eval

* fix: add required pypi metadata

---------

Co-authored-by: yusuf1759 <mr.adeshina.yusuf@gmail.com>
Co-authored-by: Patrick Kunzmann <padix.key@gmail.com>
Co-authored-by: Thomas Duignan <thomas.j.duignan@gmail.com>

Author: 4 people

.github/workflows/main.yaml

@@ -7,6 +7,8 @@ on:
   push:
     branches:
       - main
+concurrency:
+  group: ${{ github.workflow }}-${{ github.ref }}
 jobs:
   publish:
     name: Package

column_descriptions/posebusters_checks.tsv

@@ -27,10 +27,11 @@ repository clone.
 
 :::{note}
 We currently only support a Linux environment.
-`plinder` uses `openstructure` for some of its functionality and is available from the
+`plinder.data` uses `openstructure` for some of its functionality and is available from the
 `aivant` conda channel using `conda install aivant::openstructure`, but it is only built
-targeting Linux architectures.
-For Windows and MacOS users, please see the relevant
+targeting Linux architectures. It additionally uses `networkit>=11.0`, which at the time of writing,
+does not install cleanly on MacOS. `plinder.eval` also relies on `openstructure` for metrics
+calculations. For Windows and MacOS users, please see the relevant
 [_Docker_](#docker-target) resources.
 :::
 

docs/contribution/development.md

@@ -33,6 +33,18 @@ dependencies = [
     "mols2grid",
     "six",
 ]
+description = "PLINDER: The Protein-Ligand INteraction Dataset and Evaluation Resource"
+readme = "README.md"
+requires-python = ">=3.9"
+classifiers = [
+    "Programming Language :: Python :: 3",
+    "License :: OSI Approved :: Apache Software License",
+    "Operating System :: OS Independent",
+]
+
+[project.urls]
+Homepage = "https://github.com/plinder-org/plinder"
+Issues = "https://github.com/plinder-org/plinder/issues"
 
 [project.scripts]
 plinder_download = "plinder.core.index.utils:download_plinder_cmd"

docs/dataset.md

@@ -4,26 +4,16 @@
 
 try:
     import ost  # noqa
-except (ImportError, ModuleNotFoundError):
-    raise ImportError(
-        dedent(
-            """\
-            plinder.data requires the OpenStructureToolkit >= 2.8.0 (ost) to be installed.
-            Please refer to the documentation for installation instructions and current limitations.
-            See the details here: https://plinder-org.github.io/plinder/contribution/development.html
-            """
-        )
-    )
-
-try:
     import networkit  # noqa
 except (ImportError, ModuleNotFoundError):
     raise ImportError(
         dedent(
             """\
-            plinder.data requires the networkit >= 11.0 library to be installed.
+            plinder.data requires the OpenStructureToolkit >= 2.8.0 (ost) and networkit >= 11.0 to be installed.
             Please refer to the documentation for installation instructions and current limitations.
-            See the details here: https://plinder-org.github.io/plinder/contribution/development.html
+            See details here:
+
+                https://plinder-org.github.io/plinder/contribution/development.html#creating-the-conda-environment
             """
         )
     )

pyproject.toml

@@ -10,7 +10,9 @@
             """\
             plinder.eval requires the OpenStructureToolkit >= 2.8.0 (ost) to be installed.
             Please refer to the documentation for installation instructions and current limitations.
-            See the details here: https://plinder-org.github.io/plinder/contribution/development.html
+            See details here:
+
+                https://plinder-org.github.io/plinder/contribution/development.html#creating-the-conda-environment
             """
         )
     )