squashing colab int commits

README.md

@@ -119,18 +119,33 @@ A REPIC Docker image is published on both [DockerHub](https://hub.docker.com/r/c
 2. [Install and set up NVIDIA Container Toolkit](https://docs.nvidia.com/datacenter/cloud-native/container-toolkit/latest/install-guide.html) for building and running GPU-accelerated containers
 3. Pull REPIC Docker image and convert to Singularity image format (SIF) (requires >8 Gb of memory and ~40 mins for conversion):
 ```
-apptainer pull docker://cjfcameron/repic:main
+apptainer pull docker://cjfcameron/repic
 ```
 If SIF file creation is taking a long time, increase the ```mksquashfs mem``` parameter in the Apptainer config file (apptainer.conf). See [here](https://apptainer.org/docs/admin/1.0/configfiles.html) for more information.
 
 4. Run container with GPU acceleration (example [iter_pick.py](https://github.com/ccameron/REPIC/blob/main/repic/commands/iter_pick.py) command shown below):
 ```
-apptainer run --nv --bind <file_path>/REPIC/examples:/examples repic_main.sif repic iter_pick /examples/10057/iter_config.json 4 100
+apptainer run --nv --bind <file_path>/REPIC/examples:/examples repic_latest.sif repic iter_pick /examples/10057/iter_config.json 4 100
 ```
 </p></details>
 
+**<details><summary>Run using Google Colab</summary><p>**
+
+A [Jupyter Notebook](https://jupyter.org/) for installing and running REPIC on [Google Colab](https://colab.google/) is included in the REPIC GitHub repo: [repic_colab.ipynb](https://github.com/ccameron/REPIC/blob/main/repic_colab.ipynb)
+
+To open the notebook in Google Colab:
+
+1. Navigate a browser to: https://colab.google/
+2. Select "Open Colab", then "GitHub"
+3. Enter the REPIC GitHub web URL: https://github.com/ccameron/REPIC.git
+4. Select the "repic_colab.ipynb" Jupyter Notebook
+
+</p></details>
+
 **<details><summary>Run using Scipion plugin</summary><p>**
 
+:warning: **WARNING**: Scipion plugin currently only contains REPIC one-shot mode
+
 REPIC is available as a [Scipion](https://scipion.i2pc.es/)  plugin: [https://github.com/scipion-em/scipion-em-repic](https://github.com/scipion-em/scipion-em-repic)
 
 See [here](https://scipion-em.github.io/docs/release-3.0.0/docs/scipion-modes/how-to-install.html#installing-other-plugins) for information about installing plugins for Scipion.
@@ -188,7 +203,7 @@ repic iter_config examples/10057/ 176 224 <file_path>/gmodel_phosnet_202005_N63_
 
 A configuration file ``` iter_config.json ``` will be created in the current working directory.
 
-3. Pick particles by iterative ensemble learning using a Python script wrapper [iter_pick.py](https://github.com/ccameron/REPIC/blob/main/repic/commands/iter_pick.py) of [run.sh](https://github.com/ccameron/REPIC/blob/main/repic/iterative_particle_picking/run.sh) (expected run time: 20-30 min/iteration):
+3. Pick particles by iterative ensemble learning using [iter_pick.py](https://github.com/ccameron/REPIC/blob/main/repic/commands/iter_pick.py), a wrapper of [run.sh](https://github.com/ccameron/REPIC/blob/main/repic/iterative_particle_picking/run.sh) (expected run time: 20-30 min/iteration):
 
 ```
 repic iter_pick ./iter_config.json 4 100
@@ -273,7 +288,7 @@ done
 
 ` <relion_path>/relion/CtfFind/job00[0-9]/*<mrc_suffix> ` should list all CTFFIND4 output files in RELION's ` CtfFind/ `.
 
-2. Iteratively pick particles using a Python script wrapper [iter_pick.py](https://github.com/ccameron/REPIC/blob/main/repic/commands/iter_pick.py) of [run.sh](https://github.com/ccameron/REPIC/blob/main/repic/iterative_particle_picking/run.sh):
+2. Iteratively pick particles using [iter_pick.py](https://github.com/ccameron/REPIC/blob/main/repic/commands/iter_pick.py), a wrapper of [run.sh](https://github.com/ccameron/REPIC/blob/main/repic/iterative_particle_picking/run.sh):
 ```
 usage: repic iter_pick [-h] [--semi_auto] [--score] [--out_file_path OUT_FILE_PATH] config_file num_iter train_size
 
@@ -308,6 +323,9 @@ For other concerns, please email [Christopher JF Cameron](mailto:christopher.cam
 
 ## Releases
 
+### new
+  - Google Colab integrated
+
 ### v0.2.1
  - Scipion plugin created
  - Docker/Singularity/Apptainer integrated

conda-build/meta.yaml

@@ -6,15 +6,14 @@ package:
 
 source:
   url:                https://github.com/ccameron/REPIC/archive/v{{ version }}.zip
-  sha256:             1c6a1701ecc58e4732d82a3b8ef20b473974e662e40a4c42944482aeae325c0f
+  sha256:             fd77f660bf6e1fe10138c145d2aa67b69fd4ff30f249047ee49460a185407633
 
 requirements:
   host:
     - python >=3.8.16
     - pip
-
   run:
-    - python
+    - python >=3.8.16
     - matplotlib-base >=3.2.2
     - mrcfile >=1.4.3
     - networkx >=2.8.4
@@ -29,6 +28,8 @@ build:
   entry_points:
     - repic = repic.main:main
   script:             {{ PYTHON }} -m pip install . --ignore-installed --no-deps -vv
+  run_exports:
+    - {{ pin_subpackage('repic', max_pin="x") }}
 
 test:
   commands:
@@ -39,7 +40,7 @@ about:
   license:            BSD-3-Clause
   license_family:     BSD
   license_file:       LICENSE
-  summary:            REPIC - an ensemble learning approach for cryo-EM particle picking.
+  summary:            REPIC - an ensemble learning approach to cryo-EM particle picking.
   description:        REliable PIcking by Consensus (REPIC) is an ensemble learning approach to cryogenic-electron microscopy (cryo-EM) particle picking. It identifies particles common to multiple picked particle sets (i.e., consensus particles) using graph theory and integer linear programming (ILP). Picked particle sets may be found by a human specialist (manual), template matching, mathematical function (e.g., RELION's Laplacian-of-Gaussian auto-picking), or machine-learning method. REPIC expects particle sets to be in BOX file format (*.box) where each particle has coordinates, a detection box size (in pixels), and (optional) a score [0-1].
   dev_url:            https://github.com/ccameron/REPIC
   doc_url:            https://repic.readthedocs.io/en/latest/

docs/conf.py

@@ -67,10 +67,12 @@ def get_version():
 
 extensions = [
     'autoapi.extension',
-    'sphinx.ext.napoleon'
+    'sphinx.ext.napoleon',
+    'sphinx_search.extension'
 ]
 autoapi_dirs = ['../repic']
 autoapi_type = "python"
+autoapi_ignore = ['../repic/__init__.py']
 
 templates_path = ['_templates']
 exclude_patterns = ['_build', 'Thumbs.db', '.DS_Store']

docs/environment.yml

@@ -4,10 +4,12 @@ channels:
   - conda-forge
   - defaults
 dependencies:
-  - python=3.8
+  - python
+  - pip
+  - astroid==2.15.8 # https://github.com/readthedocs/sphinx-autoapi/issues/407
   - repic
   - pandoc
-  - sphinx==6.2.1
+  - sphinx
   - sphinx_rtd_theme
   - sphinx-autoapi
   - pip: