Merge pull request #16 from JHKru/master

Separate for test data generation for compatibility with Biotite >= 1.0 and Numpy >= 2.0; Ruff formatting

Author: JHKru

.github/workflows/test.yml

@@ -3,6 +3,20 @@ name: Testing Springcraft
 on: [push, pull_request]
 
 jobs:
+  lint:
+    name: Check code style
+    runs-on: ubuntu-latest
+    steps:
+    - uses: actions/checkout@v4
+    - uses: actions/setup-python@v5
+      with:
+        python-version: "3.12"
+    - name: Install ruff
+      run: pip install ruff==0.5.2
+    - name: Check code formatting
+      run: ruff format --diff
+    - name: Lint code base
+      run: ruff check
   test:
     name: Testing
 
@@ -19,7 +33,7 @@ jobs:
           auto-update-conda: true
           python-version: '3.10'
       - name: Installing dependencies
-        run: conda install -c conda-forge poetry prody pytest r-bio3d rpy2
+        run: conda install -c conda-forge poetry pytest
       - name: Building distribution
         run: poetry build -f wheel
       - name: Installing distribution

README.rst

@@ -41,6 +41,13 @@ via *pip*:
    $ git clone https://github.com/biotite-dev/springcraft.git
    $ pip install ./springcraft
 
+A development conda environment with all required dependencies for testing
+can be installed from `environment.yml`
+
+Scripts to generate reference files for tests are stored in tests/data; 
+a separate environment to rerun these locally can be found in `test_create_data_env.yml`.
+BioPhysConnectoR has to be installed separately. 
+
 Example
 =======
 

doc/conf.py

@@ -4,32 +4,34 @@
 
 __author__ = "Patrick Kunzmann"
 
-from os.path import realpath, dirname, join
-import types
 import sys
+import types
+from os.path import dirname, join, realpath
+
+import scraper
+import springcraft
 
 # Include 'src/' in PYTHONPATH
 # in order to import the 'Ammolite' package
 doc_path = dirname(realpath(__file__))
 package_path = join(dirname(doc_path), "src")
 sys.path.insert(0, package_path)
-import springcraft
 
 # Include springcraft/doc in PYTHONPATH
 # in order to import modules for example generation etc.
 sys.path.insert(0, doc_path)
-import scraper
-
 
 #### General ####
 
-extensions = ["sphinx.ext.autodoc",
-              "sphinx.ext.autosummary",
-              "sphinx.ext.doctest",
-              "sphinx.ext.mathjax",
-              "sphinx.ext.viewcode",
-              "sphinx_gallery.gen_gallery",
-              "numpydoc"]
+extensions = [
+    "sphinx.ext.autodoc",
+    "sphinx.ext.autosummary",
+    "sphinx.ext.doctest",
+    "sphinx.ext.mathjax",
+    "sphinx.ext.viewcode",
+    "sphinx_gallery.gen_gallery",
+    "numpydoc",
+]
 
 templates_path = ["templates"]
 source_suffix = [".rst"]
@@ -42,9 +44,7 @@
 exclude_patterns = ["build"]
 
 numpydoc_show_class_members = False
-autodoc_default_options = {
-    "show-inheritance": True
-}
+autodoc_default_options = {"show-inheritance": True}
 
 pygments_style = "sphinx"
 
@@ -68,41 +68,47 @@
 html_favicon = "static/assets/springcraft_logo_32p.png"
 htmlhelp_basename = "SpringcraftDoc"
 html_theme_options = {
-    "description"   : "Investigate molecular dynamics by elastic network models",
-    "logo"          : "assets/springcraft_logo.svg",
-    "logo_name"     : "true",
-    "github_user"   : "biotite-dev",
-    "github_repo"   : "springcraft",
-    "github_banner" : "true",
-    "github_type"   : "star",
-    "fixed_sidebar" : "true",
-    "page_width"    : "1200px",
+    "description": "Investigate molecular dynamics by elastic network models",
+    "logo": "assets/springcraft_logo.svg",
+    "logo_name": "true",
+    "github_user": "biotite-dev",
+    "github_repo": "springcraft",
+    "github_banner": "true",
+    "github_type": "star",
+    "fixed_sidebar": "true",
+    "page_width": "1200px",
 }
 sphinx_gallery_conf = {
-    "examples_dirs"             : "examples/scripts",
-    "gallery_dirs"              : "examples/gallery",
-    'filename_pattern'          : "",
-    "download_all_examples"     : False,
+    "examples_dirs": "examples/scripts",
+    "gallery_dirs": "examples/gallery",
+    "filename_pattern": "",
+    "download_all_examples": False,
     # Never report run time
-    "min_reported_time"         : sys.maxsize,
-    "image_scrapers"            : ("matplotlib", scraper.pymol_scraper,),
+    "min_reported_time": sys.maxsize,
+    "image_scrapers": (
+        "matplotlib",
+        scraper.pymol_scraper,
+    ),
     # Replace 'ammolite.show()'
-    "reset_modules"             : (scraper.overwrite_display_func,),
+    "reset_modules": (scraper.overwrite_display_func,),
     # Do not capture file path string output
     # by the overwritten 'ammolite.show()'
-    "capture_repr"              : (),
+    "capture_repr": (),
 }
 
 
 #### App setup ####
 
+
 def skip_non_methods(app, what, name, obj, skip, options):
     if skip:
         return True
     if what == "class":
         # Functions
         if type(obj) in [
-            types.FunctionType, types.BuiltinFunctionType, types.MethodType
+            types.FunctionType,
+            types.BuiltinFunctionType,
+            types.MethodType,
         ]:
             return False
         return True

doc/examples/scripts/basic_nma.py

@@ -1,23 +1,22 @@
 """
 Basic NMA of a Protein-ENM
 ==========================
-In this example script, a basic normal mode analysis (NMA) of a protein 
+In this example script, a basic normal mode analysis (NMA) of a protein
 coarse-grained elastic network model (ENM) is conducted.
 """
 
 
 # Code source: Jan Krumbach
 # License: BSD 3 clause
 
-import numpy as np
-import matplotlib.pyplot as plt
 import biotite
+import biotite.database.rcsb as rcsb
 import biotite.structure as struc
 import biotite.structure.io.mmtf as mmtf
-import biotite.database.rcsb as rcsb
+import matplotlib.pyplot as plt
+import numpy as np
 import springcraft
 
-
 # Fetch G:T/U Mismatch-specific DNA glycosylase from E. coli
 PDB_ID = "1MUG"
 mmtf_file = mmtf.MMTFFile.read(rcsb.fetch(PDB_ID, "mmtf"))
@@ -30,7 +29,7 @@
 eanm = springcraft.ANM(ca, ff)
 
 ## NMA
-# Compute eigenvalues and eigenvectors. 
+# Compute eigenvalues and eigenvectors.
 # The first 6 eigenvals./eigenvecs corresponding to trivial modes are omitted.
 # -> analyse modes 7-107
 eigenval, eigenvec = eanm.eigen()
@@ -49,9 +48,9 @@
 
 biotite_c = biotite.colors["orange"]
 
-ax00.bar(x=np.arange(7, len(eigenval)+7), height=eigenval, color=biotite_c)
-ax01.bar(x=np.arange(7, len(freq)+7), height=freq, color=biotite_c)
-ax1.bar(x=np.arange(1, len(msqf)+1), height=msqf, color=biotite_c) 
+ax00.bar(x=np.arange(7, len(eigenval) + 7), height=eigenval, color=biotite_c)
+ax01.bar(x=np.arange(7, len(freq) + 7), height=freq, color=biotite_c)
+ax1.bar(x=np.arange(1, len(msqf) + 1), height=msqf, color=biotite_c)
 
 ax00.set_xlabel("Mode", size=16)
 ax00.set_ylabel(r"Eigenvalue $\lambda$", size=16)

doc/examples/scripts/normal_mode.py

@@ -9,14 +9,13 @@
 # Code source: Patrick Kunzmann
 # License: BSD 3 clause
 
-import numpy as np
+import ammolite
+import biotite.database.rcsb as rcsb
 import biotite.structure as struc
 import biotite.structure.io.mmtf as mmtf
-import biotite.database.rcsb as rcsb
-import ammolite
+import numpy as np
 import springcraft
 
-
 PNG_SIZE = (800, 800)
 
 
@@ -37,8 +36,7 @@
 
 # Filter first peptide chain
 protein_chain = structure[
-    struc.filter_amino_acids(structure)
-    & (structure.chain_id == structure.chain_id[0])
+    struc.filter_amino_acids(structure) & (structure.chain_id == structure.chain_id[0])
 ]
 # Filter CA atoms
 ca_mask = (protein_chain.atom_name == "CA") & (protein_chain.element == "C")
@@ -57,15 +55,28 @@
 pymol_object.show_as("cartoon")
 # Show eigenvectors as arrows
 ammolite.draw_arrows(
-    ca.coord, ca.coord + vector,
-    radius=0.2, head_radius=0.4, head_length=1.0
+    ca.coord, ca.coord + vector, radius=0.2, head_radius=0.4, head_length=1.0
+)
+ammolite.cmd.set_view(
+    (
+        0.605540633,
+        0.363677770,
+        -0.707855821,
+        -0.416691631,
+        0.902691007,
+        0.107316799,
+        0.678002179,
+        0.229972601,
+        0.698157668,
+        0.000000000,
+        0.000000000,
+        -115.912551880,
+        32.098876953,
+        31.005725861,
+        78.377349854,
+        89.280677795,
+        142.544403076,
+        -20.000000000,
+    )
 )
-ammolite.cmd.set_view((
-     0.605540633,    0.363677770,   -0.707855821,
-    -0.416691631,    0.902691007,    0.107316799,
-     0.678002179,    0.229972601,    0.698157668,
-     0.000000000,    0.000000000, -115.912551880,
-    32.098876953,   31.005725861,   78.377349854,
-    89.280677795,  142.544403076,  -20.000000000
-))
-ammolite.show(PNG_SIZE)
+ammolite.show(PNG_SIZE)

doc/scraper.py

@@ -1,15 +1,16 @@
-from glob import glob
+import datetime
 import shutil
 import tempfile
-import datetime
+import time
 from os.path import getsize
+
 from sphinx_gallery.scrapers import figure_rst
 
 NO_ASSIGN = "___"
 
 
 def pymol_scraper(block, block_vars, gallery_conf):
-    block_type,_, _ = block
+    block_type, _, _ = block
     if block_type == "code":
         globals = block_vars["example_globals"]
         # Look for replaced show() output:
@@ -20,54 +21,54 @@ def pymol_scraper(block, block_vars, gallery_conf):
             image_path = globals[NO_ASSIGN]
             # Copy the images into the 'gallery' directory under a canonical
             # sphinx-gallery name
-            image_path_iterator = block_vars['image_path_iterator']
+            image_path_iterator = block_vars["image_path_iterator"]
             image_destination = image_path_iterator.next()
             shutil.copy(image_path, image_destination)
-            return figure_rst([image_destination], gallery_conf['src_dir'])
-    return figure_rst([], gallery_conf['src_dir'])
+            return figure_rst([image_destination], gallery_conf["src_dir"])
+    return figure_rst([], gallery_conf["src_dir"])
 
 
 def overwrite_display_func(gallery_conf, fname):
     import ammolite
 
     def show(size=None, use_ray=False, timeout=60.0, pymol_instance=None):
         INTERVAL = 0.1
-        
+
         if size is None:
             width = 0
             height = 0
         else:
             width, height = size
-        
+
         if use_ray:
             ray = 1
         else:
             ray = 0
-        
+
         image_file = tempfile.NamedTemporaryFile(
             delete=False, prefix="ammolite_", suffix=".png"
         )
         image_file.close()
-        
+
         start_time = datetime.datetime.now()
 
         ammolite.cmd.png(image_file.name, width, height, ray=ray)
-        
+
         while True:
             # After 'timeout' seconds the loop exits with an error
             if (datetime.datetime.now() - start_time).total_seconds() > timeout:
                 raise TimeoutError(
                     "No PNG image was output within the expected time limit"
                 )
-            
+
             # Check if PyMOL has already written image data to file
             if getsize(image_file.name) > 0:
                 break
 
             time.sleep(INTERVAL)
-        
+
         return image_file.name
 
     ammolite.show = show
     ammolite.cmd.reinitialize()
-    ammolite.setup_parameters(ammolite.pymol)
+    ammolite.setup_parameters(ammolite.pymol)

environment.yml

@@ -7,9 +7,8 @@ channels:
   - conda-forge
 
 dependencies:
-  - numpy >=1.15
-  - biotite >=0.32
-  - prody >=2.1
+  - numpy >=2.0
+  - biotite >=1.0.1
   - pytest >=5.2
   - matplotlib >=3.3
   - poetry >=1.0
@@ -18,5 +17,4 @@ dependencies:
   - sphinx-gallery =0.9.0
   - numpydoc >=0.8
   - ammolite >=0.8
-  - rpy2
-  - r-bio3d
+  - ruff >=0.6.7