Merge pull request #584 from ComputationalCryoEM/develop

Develop ~~> Master

Author: garrettwrong

.bumpversion.cfg

@@ -1,5 +1,5 @@
 [bumpversion]
-current_version = 0.8.1
+current_version = 0.9.0
 commit = True
 tag = True
 

.github/workflows/workflow.yml

@@ -12,7 +12,7 @@ jobs:
     - name: Set up Python
       uses: actions/setup-python@v2
       with:
-        python-version: 3.6
+        python-version: '3.7'
     - name: Install dependencies
       run: |
         python -m pip install --upgrade pip
@@ -25,15 +25,15 @@ jobs:
     runs-on: ubuntu-latest
     strategy:
       matrix:
-        python-version: [3.6, 3.7, 3.8]
+        python-version: ['3.7', '3.8', '3.9', '3.10']
         pyenv: [stable, dev]
         exclude:
-          # Exclude 3.6-stable so we can add pre and post tasks to that environment.
-          - python-version: 3.6
+          # Exclude 3.7-stable so we can add pre and post tasks to that environment.
+          - python-version: '3.7'
             pyenv: stable
         include:
-          # Re-include 3.6-stable with additional tox tasks.
-          - python-version: 3.6
+          # Re-include 3.7-stable with additional tox tasks.
+          - python-version: '3.7'
             pyenv: stable,docs
 
 
@@ -61,7 +61,7 @@ jobs:
     - name: Setup Python
       uses: actions/setup-python@v2
       with:
-        python-version: 3.6
+        python-version: '3.7'
     - name: Install Dependencies
       run: |
         python -m pip install --upgrade pip

CONTRIBUTORS.rst

@@ -9,29 +9,35 @@ Developers of the Python and Matlab collection of ASPIRE codes are listed below.
 
 .. table:: Python Contributors
 
-   +------------------+--------------+---------------------------+----------------------+
-   | Name             | GithubID     | Email                     | Affiliations         |
-   +==================+==============+===========================+======================+
-   | Joakim Andén     | janden       | [email protected]             | Princeton University |
-   +------------------+--------------+---------------------------+----------------------+
-   | Vineet Bansal    | vineetbansal | [email protected]     | Princeton University |
-   +------------------+--------------+---------------------------+----------------------+
-   | Robbie Brook     | rbrook       | [email protected]          | Princeton University |
-   +------------------+--------------+---------------------------+----------------------+
-   | Ayelet Heimowitz | ayeltg       | [email protected]     | Princeton University |
-   +------------------+--------------+---------------------------+----------------------+
-   | Gabi Pragier     | pgabi        | [email protected]     | Tel Aviv University  |
-   +------------------+--------------+---------------------------+----------------------+
-   | Itay Sason       | itaysason    | [email protected]  | Tel Aviv University  |
-   +------------------+--------------+---------------------------+----------------------+
-   | Yoel Shkolnisky  | yoelsh       | [email protected]    | Tel Aviv University  |
-   +------------------+--------------+---------------------------+----------------------+
-   | Amit Singer      | amitsinger   | [email protected]       | Princeton University |
-   +------------------+--------------+---------------------------+----------------------+
-   | Garrett Wright   | garrettwrong | [email protected]    | Princeton University |
-   +------------------+--------------+---------------------------+----------------------+
-   | Junchao Xia      | junchaoxia   | [email protected] | Princeton University |
-   +------------------+--------------+---------------------------+----------------------+
+   +------------------+-----------------+---------------------------+-----------------------------------+
+   | Name             | GithubID        | Email                     | Affiliations                      |
+   +==================+=================+===========================+===================================+
+   | Joakim Andén     | janden          | [email protected]             | KTH Royal Institute of Technology |
+   +------------------+-----------------+---------------------------+-----------------------------------+
+   | Vineet Bansal    | vineetbansal    | [email protected]     | Princeton University              |
+   +------------------+-----------------+---------------------------+-----------------------------------+
+   | Robbie Brook     | rbrook          | [email protected]          | Princeton University              |
+   +------------------+-----------------+---------------------------+-----------------------------------+
+   | Josh Carmichael  | j-c-c           | [email protected]  | Princeton University              |
+   +------------------+-----------------+---------------------------+-----------------------------------+
+   | Ayelet Heimowitz | ayeltg          | [email protected]       | Ariel University                  |
+   +------------------+-----------------+---------------------------+-----------------------------------+
+   | Chris Langfield  | chris-langfield | [email protected]   | Princeton University              |
+   +------------------+-----------------+---------------------------+-----------------------------------+
+   | Amit Moscovich   | mosco           | [email protected]     | Tel Aviv University               |
+   +------------------+-----------------+---------------------------+-----------------------------------+
+   | Gabi Pragier     | pgabi           | [email protected]     | Tel Aviv University               |
+   +------------------+-----------------+---------------------------+-----------------------------------+
+   | Itay Sason       | itaysason       | [email protected]  | Tel Aviv University               |
+   +------------------+-----------------+---------------------------+-----------------------------------+
+   | Yoel Shkolnisky  | yoelsh          | [email protected]    | Tel Aviv University               |
+   +------------------+-----------------+---------------------------+-----------------------------------+
+   | Amit Singer      | amitsinger      | [email protected]       | Princeton University              |
+   +------------------+-----------------+---------------------------+-----------------------------------+
+   | Garrett Wright   | garrettwrong    | [email protected]    | Princeton University              |
+   +------------------+-----------------+---------------------------+-----------------------------------+
+   | Junchao Xia      | junchaoxia      | [email protected] | Princeton University              |
+   +------------------+-----------------+---------------------------+-----------------------------------+
 
 |
 

README.md

@@ -3,8 +3,9 @@
 [![Azure Build Status](https://dev.azure.com/ComputationalCryoEM/Aspire-Python/_apis/build/status/ComputationalCryoEM.ASPIRE-Python?branchName=master)](https://dev.azure.com/ComputationalCryoEM/Aspire-Python/_build/latest?definitionId=3&branchName=master)
 [![Github Actions Status](https://github.com/ComputationalCryoEM/ASPIRE-Python/actions/workflows/workflow.yml/badge.svg)](https://github.com/ComputationalCryoEM/ASPIRE-Python/actions/workflows/workflow.yml)
 [![codecov](https://codecov.io/gh/ComputationalCryoEM/ASPIRE-Python/branch/master/graph/badge.svg?token=3XFC4VONX0)](https://codecov.io/gh/ComputationalCryoEM/ASPIRE-Python)
+[![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.5657281.svg)](https://doi.org/10.5281/zenodo.5657281)
 
-# ASPIRE - Algorithms for Single Particle Reconstruction - v0.8.1
+# ASPIRE - Algorithms for Single Particle Reconstruction - v0.9.0
 
 This is the Python version to supersede the [Matlab ASPIRE](https://github.com/PrincetonUniversity/aspire).
 
@@ -14,17 +15,24 @@ processing pipeline, including 3-D *ab-initio* modeling, 2-D class averaging, au
 
 For more information about the project, algorithms, and related publications please refer to the [ASPIRE Project website](http://spr.math.princeton.edu/).
 
-**For full documentation see [the docs](https://computationalcryoem.github.io/ASPIRE-Python).**
+**For full documentation and tutorials see [the docs](https://computationalcryoem.github.io/ASPIRE-Python).**
+
+Please cite using the following DOI. This DOI represents all versions, and will always resolve to the latest one.
+
+```
+ComputationalCryoEM/ASPIRE-Python: v0.9.0 https://doi.org/10.5281/zenodo.5657281
+
+```
 
 ## Installation Instructions
 
 For end-users
 -------------
 
-ASPIRE is a pip-installable package that works on Linux/Mac/Windows, and requires Python 3.6. The simplest option is to use Anaconda 64-bit for your platform with a minimum of Python 3.6 and `pip`, and then use `pip` to install `aspire` in that environment.
+ASPIRE is a pip-installable package that works on Linux/Mac/Windows, and requires Python 3.7. The simplest option is to use Anaconda 64-bit for your platform with a minimum of Python 3.7 and `pip`, and then use `pip` to install `aspire` in that environment.
 
 ```
-conda create -n aspire_env python=3.6 pip
+conda create -n aspire_env python=3.7 pip
 conda activate aspire_env
 pip install aspire
 ```
@@ -53,7 +61,7 @@ pip install -e ".[dev]"
 
 ```
 
-If you prefer not to use Anaconda, or want to manage environments yourself, you should be able to use `pip` with Python >= 3.6.
+If you prefer not to use Anaconda, or want to manage environments yourself, you should be able to use `pip` with Python >= 3.7.
 Please see the full documentation for details.
 
 You may optionally install additional packages for GPU extensions:

azure-pipelines.yml

@@ -14,8 +14,8 @@ jobs:
     vmImage: 'ubuntu-latest'
   strategy:
     matrix:
-      Python36:
-        python.version: '3.6'
+      Python37:
+        python.version: '3.7'
 
   steps:
   - bash: echo "##vso[task.prependpath]$CONDA/bin"
@@ -36,8 +36,8 @@ jobs:
     vmImage: 'ubuntu-18.04'
   strategy:
     matrix:
-      Python36:
-        python.version: '3.6'
+      Python37:
+        python.version: '3.7'
 
   steps:
   - bash: echo "##vso[task.prependpath]$CONDA/bin"
@@ -61,8 +61,8 @@ jobs:
     vmImage: 'macOS-latest'
   strategy:
     matrix:
-      Python36:
-        python.version: '3.6'
+      Python37:
+        python.version: '3.7'
 
   steps:
   - bash: |
@@ -86,13 +86,13 @@ jobs:
     displayName: pytest
 
 - job:
-  displayName: macOS-10.14
+  displayName: macOS-10.15
   pool:
-    vmImage: 'macOS-10.14'
+    vmImage: 'macOS-10.15'
   strategy:
     matrix:
-      Python36:
-        python.version: '3.6'
+      Python37:
+        python.version: '3.7'
 
   steps:
   - bash: |
@@ -121,8 +121,8 @@ jobs:
     vmImage: 'windows-latest'
   strategy:
     matrix:
-      Python36:
-        python.version: '3.6'
+      Python37:
+        python.version: '3.7'
 
   steps:
   - powershell: Write-Host "##vso[task.prependpath]$env:CONDA\Scripts"
@@ -139,28 +139,3 @@ jobs:
       pip install -e .[dev]
       pytest --random-order 
     displayName: pytest
-
-- job:
-  displayName: vs2017-win2016
-  pool:
-    vmImage: 'vs2017-win2016'
-  strategy:
-    matrix:
-      Python36:
-        python.version: '3.6'
-
-  steps:
-  - powershell: Write-Host "##vso[task.prependpath]$env:CONDA\Scripts"
-    displayName: Add conda to PATH
-
-  - script: conda env create --name myEnvironment --file environment.yml
-    displayName: Create Anaconda environment
-
-  - script: conda update -q -y conda
-    displayName: Update conda
-
-  - script: |
-      call activate myEnvironment
-      pip install -e .[dev]
-      pytest --random-order
-    displayName: pytest

docs/source/conf.py

@@ -49,7 +49,7 @@
      'gallery_dirs': ['auto_tutorials', 'auto_experiments'],  # path to where to save gallery generated output
      'download_all_examples': False,
      'within_subsection_order': ExampleTitleSortKey,
-     'filename_pattern': '/*.py',
+     'filename_pattern': r'/tutorials/.*\.py',  # Parse all gallery python files, but only execute tutorials.
 }
 
 # Add any paths that contain templates here, relative to this directory.
@@ -74,7 +74,7 @@
 # built documents.
 #
 # The full version, including alpha/beta/rc tags.
-release = version = "0.8.1"
+release = version = "0.9.0"
 
 # 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 v0.8.1
+Aspire v0.9.0
 ==============
 
 Algorithms for Single Particle Reconstruction

docs/source/installation.rst

@@ -1,7 +1,7 @@
 Installation
 ============
 
-ASPIRE is based on Python 3.6, and comes with an ``environment.yml`` for reconstructing a working Conda environment to run the package.
+ASPIRE is based on Python 3.7, and comes with an ``environment.yml`` for reconstructing a working Conda environment to run the package.
 The package is tested on Linux/Windows/Mac OS X. Pre-built binaries are available for all platform-specific components. No manual
 compilation should be needed.
 
@@ -32,7 +32,7 @@ Finally, we install the ``aspire`` package inside the activated environment. Thi
 
 ::
 
-   conda create --name aspire_env python=3.6 pip
+   conda create --name aspire_env python=3.7 pip
    conda activate aspire_env
    pip install aspire
 
@@ -73,7 +73,7 @@ We recommend using ``conda`` or a ``virtualenv`` environment managing solutions
 Again, we recommend the above for consistency.
 However, ASPIRE is a ``pip`` package,
 so you can attempt to install it using standard ``pip`` or ``setup.py`` commands.  There are methods such as ``pip --no-deps`` that can leave your other packages undisturbed, but this is left to the developer.
-ASPIRE should generally be compatible with newer version of Python, and newer dependent packages. We are currently testing 3.6, 3.7, 3.8 base Python as configured by ASPIRE, and with upgrading packages to the latest for each of those bases.
+ASPIRE should generally be compatible with newer version of Python, and newer dependent packages. We are currently testing 3.7, 3.8, 3.9, and 3.10 base Python as configured by ASPIRE, and with upgrading packages to the latest for each of those bases.
 If you encounter an issue with a custom pip install, we will try to help, but you may be on your own for support of this method of installation.
 
 ::

docs/source/quickstart.rst

@@ -16,7 +16,7 @@ Currently, the following operations can be run with ASPIRE:
 1. Particle-Picking
 ###################
 
-The ``apple`` command takes in a folder of one or more ``*.mrc`` files, picks particles using the Apple-Picker algorithm described at
+The ``apple`` command takes in a file or folder of one or more ``*.mrc`` files, picks particles using the Apple-Picker algorithm described at
 :cite:`DBLP:journals/corr/abs-1802-00469`, and generates ``*.star`` files, one for each ``*.mrc`` file processed, at an output folder location.
 
 For example, to run the command on sample data included in ASPIRE (a single ``sample.mrc`` file provided from the 5.3 GB
@@ -26,7 +26,7 @@ For example, to run the command on sample data included in ASPIRE (a single ``sa
 .. code-block:: console
 
     mkdir apple_output
-    aspire apple --mrc_file /path/to/aspire/data/sample.mrc --output_dir particles
+    aspire apple --mrc_path /path/to/aspire/data/sample.mrc --output_dir particles
 
 Use the ``--help`` argument with the command to see the several options associated with this command.
 

environment.yml

@@ -7,7 +7,7 @@ channels:
 dependencies:
   - fftw
   - pip
-  - python=3.6
+  - python=3.7
   - pip:
     - .