From 7e921353c7cb5cd5f5ad7b429749965c618e4dd1 Mon Sep 17 00:00:00 2001
From: Patrick Kunzmann <padix.key@gmail.com>
Date: Fri, 20 Dec 2024 10:39:13 +0100
Subject: [PATCH] Update CI and docs for new CCD build process

---
 .github/workflows/test_and_deploy.yml | 6 +++---
 doc/install.rst                       | 9 ++++-----
 pyproject.toml                        | 3 +--
 src/biotite/setup_ccd.py              | 4 +---
 src/biotite/structure/info/ccd.py     | 4 ++--
 5 files changed, 11 insertions(+), 15 deletions(-)

diff --git a/.github/workflows/test_and_deploy.yml b/.github/workflows/test_and_deploy.yml
index 85937ceb0..e532d3c70 100644
--- a/.github/workflows/test_and_deploy.yml
+++ b/.github/workflows/test_and_deploy.yml
@@ -72,14 +72,14 @@ jobs:
         id: cache-ccd
         with:
           path: ./src/biotite/structure/info/components.bcif
-          key: cache-${{ hashFiles('setup_ccd.py') }}-${{ hashFiles('components.cif.gz') }}
+          key: cache-${{ hashFiles('src/biotite/setup_ccd.py') }}-${{ hashFiles('components.cif.gz') }}
       - name: Remove CCD used for hashing
         run: rm components.cif.gz
       - name: Build internal CCD
         if: steps.cache-ccd.outputs.cache-hit != 'true'
         run: |
-          pip install .
-          python setup_ccd.py
+          pip install -e .
+          python -m biotite.setup_ccd
       - name: Install build backend
         run: pip install build
       - name: Build distribution
diff --git a/doc/install.rst b/doc/install.rst
index 8b468e0a5..d314ae05f 100644
--- a/doc/install.rst
+++ b/doc/install.rst
@@ -57,10 +57,10 @@ You can also install *Biotite* from the
 `project repository <https://github.com/biotite-dev/biotite>`_.
 However, in addition to building and installing the package, the internal
 `Chemical Component Dictionary (CCD) <https://www.wwpdb.org/data/ccd>`_. for
-:mod:`biotite.structure.info` needs to be built with the ``setup_ccd.py`` script.
+:mod:`biotite.structure.info` needs to be built with the ``setup_ccd`` module.
 The script in turn requires *Biotite*.
 The solution to this chicken-and-egg problem is to first install Biotite without the
-CCD, then build the CCD and finally install Biotite again.
+CCD and build the CCD afterwards.
 After cloning the repository, navigate to its top-level directory (the one
 ``setup.py`` is in) and type the following:
 
@@ -68,10 +68,9 @@ After cloning the repository, navigate to its top-level directory (the one
 
    $ pip install .
    $ python -m biotite.setup_ccd
-   $ pip install .
 
-The `setup_ccd.py` script can also be used to update the internal CCD to the current
-upstream version from the PDB.
+``setup_ccd.py`` can also be used to update the internal CCD to the current upstream
+version from the PDB.
 
 Having the *Biotite* installation always pointing to your repository clone is
 also possible.
diff --git a/pyproject.toml b/pyproject.toml
index 2f8f47181..2c6ae641a 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -58,7 +58,7 @@ ignore = [
 
 [tool.ruff.lint.per-file-ignores]
 # Due to `* import` of BCIF encoding
-"setup_ccd.py" = ["F405", "F403"]
+"src/biotite/setup_ccd.py" = ["F405", "F403"]
 # Due to imports after the PATH has been adjusted
 "doc/conf.py" = ["E402"]
 # Due to `from .module import *` imports in `__init__.py` modules
@@ -109,7 +109,6 @@ exclude = [
   "benchmarks",
   "doc",
   "environment.yml",
-  "setup_ccd.py",
   # .github, .gitignore, .gitattributes
   ".git*",
 ]
diff --git a/src/biotite/setup_ccd.py b/src/biotite/setup_ccd.py
index 162ed7561..0032dfcfb 100644
--- a/src/biotite/setup_ccd.py
+++ b/src/biotite/setup_ccd.py
@@ -7,9 +7,7 @@
 import requests
 from biotite.structure.io.pdbx import *
 
-OUTPUT_CCD = (
-    Path(__file__).parent / "structure" / "info" / "components.bcif"
-)
+OUTPUT_CCD = Path(__file__).parent / "structure" / "info" / "components.bcif"
 CCD_URL = "https://files.wwpdb.org/pub/pdb/data/monomers/components.cif.gz"
 
 
diff --git a/src/biotite/structure/info/ccd.py b/src/biotite/structure/info/ccd.py
index adcbc92f0..8c791b554 100644
--- a/src/biotite/structure/info/ccd.py
+++ b/src/biotite/structure/info/ccd.py
@@ -53,7 +53,7 @@ def get_ccd():
         return BinaryCIFFile.read(_CCD_FILE).block
     except FileNotFoundError:
         raise RuntimeError(
-            "Internal CCD not found. Please run 'setup_ccd.py' and reinstall Biotite."
+            "Internal CCD not found. Please run 'python -m biotite.setup_ccd'."
         )
 
 
@@ -68,7 +68,7 @@ def set_ccd_path(ccd_path):
     ----------
     ccd_path : path-like
         The path to the custom CCD in BinaryCIF format, prepared with the
-        ``setup_ccd.py`` script.
+        ``setup_ccd.py`` module.
 
     Notes
     -----