develop ~~> main v0.12.1

.bumpversion.cfg

@@ -1,5 +1,5 @@
 [bumpversion]
-current_version = 0.12.0
+current_version = 0.12.1
 commit = True
 tag = True
 

.github/workflows/long_workflow.yml

@@ -9,6 +9,7 @@ on:
 jobs:
   expensive_tests:
     runs-on: self-hosted
+    timeout-minutes: 360
     steps:
     - uses: actions/checkout@v3
     - name: Install dependencies

.github/workflows/workflow.yml

@@ -155,7 +155,7 @@ jobs:
     - name: Cache Data
       run: |
         ASPIREDIR=${{ env.WORK_DIR }} python -c \
-        "import aspire; print(aspire.config['common']['cache_dir']); aspire.downloader.emdb_2660()"
+        "import aspire; print(aspire.config['common']['cache_dir']); import aspire.downloader; aspire.downloader.emdb_2660()"
     - name: Cleanup
       run: rm -rf ${{ env.WORK_DIR }}
 

README.md

@@ -5,7 +5,7 @@
 [![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.5657281.svg)](https://doi.org/10.5281/zenodo.5657281)
 [![Downloads](https://static.pepy.tech/badge/aspire/month)](https://pepy.tech/project/aspire)
 
-# ASPIRE - Algorithms for Single Particle Reconstruction - v0.12.0
+# ASPIRE - Algorithms for Single Particle Reconstruction - v0.12.1
 
 The ASPIRE-Python project supersedes [Matlab ASPIRE](https://github.com/PrincetonUniversity/aspire).
 
@@ -20,7 +20,7 @@ For more information about the project, algorithms, and related publications ple
 Please cite using the following DOI. This DOI represents all versions, and will always resolve to the latest one.
 
 ```
-ComputationalCryoEM/ASPIRE-Python: v0.12.0 https://doi.org/10.5281/zenodo.5657281
+ComputationalCryoEM/ASPIRE-Python: v0.12.1 https://doi.org/10.5281/zenodo.5657281
 
 ```
 

docs/check_docstrings.py

@@ -0,0 +1,62 @@
+import logging
+import os
+import re
+import sys
+from glob import glob
+
+logger = logging.getLogger(__name__)
+
+
+def check_blank_line_above_param_section(file_path):
+    """
+    Check that every docstring with both a body section and a parameter
+    section separates the two sections with exactly one blank line. Log
+    errors and return count.
+
+    :param file_path: File path to check for error.
+    :return: Per file error count.
+    """
+    error_count = 0
+    with open(file_path, "r") as file:
+        content = file.read()
+
+    regex = (
+        r" {4,}\"\"\"\n(?:^[^:]+?[^\n])+(\n|\n\n\n+) {4,}(:p|:r)(?:.*\n)+? {4,}\"\"\""
+    )
+
+    bad_docstrings = re.finditer(regex, content, re.MULTILINE)
+    for docstring in bad_docstrings:
+        line_number = content.count("\n", 0, docstring.start()) + 1
+
+        # Log error message.
+        msg = "Must have exactly 1 blank line between docstring body and parameter sections."
+        logger.error(f"{file_path}: {line_number}: {msg}")
+        error_count += 1
+
+    return error_count
+
+
+def process_directory(directory):
+    """
+    Recursively walk through directories and check for docstring errors.
+    If any errors found, log error count and exit.
+
+    :param directory: Directory path to walk.
+    """
+    error_count = 0
+    for file in glob(os.path.join(directory, "**/*.py"), recursive=True):
+        error_count += check_blank_line_above_param_section(file)
+    if error_count > 0:
+        logger.error(f"Found {error_count} docstring errors.")
+        sys.exit(1)
+
+
+if __name__ == "__main__":
+    if len(sys.argv) != 2:
+        logger.warning("Usage: python check_docstrings.py <directory>")
+        sys.exit(1)
+
+    target_directory = sys.argv[1]
+    if not os.path.isdir(target_directory):
+        raise RuntimeError(f"Invalid target directory path: {target_directory}")
+    process_directory(target_directory)

docs/source/conf.py

@@ -86,7 +86,7 @@
 # built documents.
 #
 # The full version, including alpha/beta/rc tags.
-release = version = "0.12.0"
+release = version = "0.12.1"
 
 # The language for content autogenerated by Sphinx. Refer to documentation
 # for a list of supported languages.

docs/source/index.rst

@@ -1,4 +1,4 @@
-Aspire v0.12.0
+Aspire v0.12.1
 ==============
 
 Algorithms for Single Particle Reconstruction

gallery/experiments/experimental_abinitio_pipeline_10028.py

@@ -30,7 +30,7 @@
 
 from aspire.abinitio import CLSyncVoting
 from aspire.basis import FFBBasis3D
-from aspire.denoising import DefaultClassAvgSource, DenoiserCov2D
+from aspire.denoising import DefaultClassAvgSource, DenoisedSource, DenoiserCov2D
 from aspire.noise import AnisotropicNoiseEstimator
 from aspire.reconstruction import MeanEstimator
 from aspire.source import OrientedSource, RelionSource
@@ -121,7 +121,7 @@
     # Use CWF denoising
     cwf_denoiser = DenoiserCov2D(src)
     # Use denoised src for classification
-    classification_src = cwf_denoiser.denoise()
+    classification_src = DenoisedSource(src, cwf_denoiser)
     # Cache for speedup.  Avoids recomputing.
     classification_src = classification_src.cache()
     # Peek, what do the denoised images look like...