Move installation to toml based.

.github/workflows/tests.yml

@@ -5,16 +5,14 @@ jobs:
   build:
     runs-on: ubuntu-latest
     steps:
-    - uses: actions/checkout@v3
-    - uses: actions/setup-python@v4
-      with:
-        python-version: '3.8'
-    - name:
-        Install dependencies
-      run: |
-        python -m pip install --upgrade pip
-        pip install pytest
-    - name: Test with pytest
-      run: |
-        pip install -e .
-        pytest
+      - uses: actions/checkout@v3
+      - uses: actions/setup-python@v4
+        with:
+          python-version: "3.8"
+      - name: Install dependencies
+        run: |
+          python -m pip install --upgrade pip
+      - name: Test with pytest
+        run: |
+          python -m pip install -e ".[test]"
+          python -m pytest -s -W ignore

.pre-commit-config.yaml

@@ -1,28 +1,45 @@
+ci:
+  autoupdate_commit_msg: "chore: update pre-commit hooks"
+  autofix_commit_msg: "style: pre-commit fixes"
+
 repos:
-    - repo: https://github.com/pycqa/isort
-      rev: 5.12.0
-      hooks:
-          - id: isort
-    - repo: https://github.com/pre-commit/pre-commit-hooks
-      rev: v4.2.0
-      hooks:
-          - id: check-docstring-first
-          - id: check-executables-have-shebangs
-          - id: check-merge-conflict
-          - id: check-toml
-          - id: end-of-file-fixer
-          - id: mixed-line-ending
-            args: [--fix=lf]
-          - id: requirements-txt-fixer
-          - id: trailing-whitespace
-            args: [--markdown-linebreak-ext=md]
-    - repo: https://github.com/PyCQA/flake8
-      rev: 6.0.0
-      hooks:
-          - id: flake8
-            # this seems to need to be here in addition to setup.cfg
-            exclude: __init__.py|examples
-    - repo: https://github.com/psf/black
-      rev: 22.3.0
-      hooks:
-          - id: black
+  - repo: https://github.com/pycqa/isort
+    rev: 5.12.0
+    hooks:
+      - id: isort
+        args: ["--profile", "black", "--filter-files"]
+
+  - repo: https://github.com/pre-commit/pre-commit-hooks
+    rev: "v4.4.0"
+    hooks:
+      - id: check-docstring-first
+      - id: check-executables-have-shebangs
+      - id: check-merge-conflict
+      - id: check-toml
+      - id: end-of-file-fixer
+      - id: mixed-line-ending
+        args: [--fix=lf]
+      - id: requirements-txt-fixer
+      - id: trailing-whitespace
+        args: [--markdown-linebreak-ext=md]
+      - id: check-added-large-files
+      - id: check-case-conflict
+      - id: check-merge-conflict
+      - id: check-symlinks
+      - id: check-yaml
+      - id: debug-statements
+      - id: end-of-file-fixer
+      - id: name-tests-test
+        args: ["--pytest-test-first"]
+      - id: requirements-txt-fixer
+
+  - repo: https://github.com/psf/black
+    rev: 22.3.0
+    hooks:
+      - id: black
+  - repo: https://github.com/pre-commit/mirrors-prettier
+    rev: "v3.0.3"
+    hooks:
+      - id: prettier
+        types_or: [yaml, markdown, html, css, scss, javascript, json]
+        args: [--prose-wrap=always]

LICENSE.md

@@ -1,10 +1,9 @@
 BSD 3-Clause License
 
-Copyright (c) 2022, Alan Turing Institute
-All rights reserved.
+Copyright (c) 2022, Alan Turing Institute All rights reserved.
 
-Redistribution and use in source and binary forms, with or without
-modification, are permitted provided that the following conditions are met:
+Redistribution and use in source and binary forms, with or without modification,
+are permitted provided that the following conditions are met:
 
 1. Redistributions of source code must retain the above copyright notice, this
    list of conditions and the following disclaimer.
@@ -13,17 +12,17 @@ modification, are permitted provided that the following conditions are met:
    this list of conditions and the following disclaimer in the documentation
    and/or other materials provided with the distribution.
 
-3. Neither the name of the copyright holder nor the names of its
-   contributors may be used to endorse or promote products derived from
-   this software without specific prior written permission.
+3. Neither the name of the copyright holder nor the names of its contributors
+   may be used to endorse or promote products derived from this software without
+   specific prior written permission.
 
-THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
-AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
-IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
-DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE
-FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL
-DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR
-SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER
-CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY,
-OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE
-OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
+THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND
+ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED
+WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
+DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE FOR
+ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES
+(INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES;
+LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON
+ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT
+(INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS
+SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.

README.md

@@ -2,31 +2,50 @@
 [![Tests](https://github.com/alan-turing-institute/affinity-vae/actions/workflows/tests.yml/badge.svg)](https://github.com/alan-turing-institute/affinity-vae/actions/workflows/tests.yml)
 [![pre-commit](https://img.shields.io/badge/pre--commit-enabled-brightgreen?logo=pre-commit&logoColor=white)](https://github.com/pre-commit/pre-commit)
 
-> Note: This a development version of the code. The code in the `main` branch is a more stable version of the code.
+> Note: This a development version of the code. The code in the `main` branch is
+> a more stable version of the code.
 
 # Affinity-VAE
 
-
-**Affinity-VAE for disentanglement, clustering and classification of objects in multidimensional image data**  
-Mirecka J, Famili M, Kotanska A, Jurashcko N, Costa-Gomes B, Palmer CM, Thiyagalingam J, Burnley T, Basham M & Lowe AR  
+**Affinity-VAE for disentanglement, clustering and classification of objects in
+multidimensional image data**  
+Mirecka J, Famili M, Kotanska A, Jurashcko N, Costa-Gomes B, Palmer CM,
+Thiyagalingam J, Burnley T, Basham M & Lowe AR  
 [![doi:10.48550/arXiv.2209.04517](https://img.shields.io/badge/doi-10.48550/arXiv.2209.04517-blue)](https://doi.org/10.48550/arXiv.2209.04517)
 
 ## Installation
 
 ### Installing with pip + virtual environments
 
-> Note: This has been tested in the `refactor` branch.
+> Note: This has been tested in the `develop` branch.
 
-You can install the libraries needed for this package on a [fresh virtual environment](https://packaging.python.org/en/latest/guides/installing-using-pip-and-virtual-environments/) with the following:
+You can install the libraries needed for this package on a
+[fresh virtual environment](https://packaging.python.org/en/latest/guides/installing-using-pip-and-virtual-environments/)
+with the following:
 
 ```
-python3 -m venv env
+python -m venv env
 source env/bin/activate
-pip install -e .
+python -m pip install --upgrade pip
+python -m pip install -e .
+```
+
+If you are developing code, you should be able to run precommits and tests,
+thefore the best installation option after setting up the virtual environment
+is:
+
+```
+python -m pip install -e ."[test]"
 ```
-> Note: This is the preffered option for running on Turing macOS laptops.
 
-> Warning: M1 macOS can not do [pytorch paralelisation](https://github.com/pytorch/pytorch/issues/70344). A temporary solution for this is to modify the code on the DataLoaders in data.py to `num_workers=0` in order to run the code. Otherwise you will get the error: `AttributeError: Can't pickle local object 'ProteinDataset.__init__.<locals>.<lambda>'`.
+> Note: This is the preferred option for running on Turing macOS laptops.
+
+> Warning: M1 macOS can not do
+> [pytorch paralelisation](https://github.com/pytorch/pytorch/issues/70344). A
+> temporary solution for this is to modify the code on the DataLoaders in
+> data.py to `num_workers=0` in order to run the code. Otherwise you will get
+> the error:
+> `AttributeError: Can't pickle local object 'ProteinDataset.__init__.<locals>.<lambda>'`.
 
 ### Installing with conda in Baskerville
 
@@ -52,10 +71,12 @@ conda install -c anaconda click
 conda install pytorch torchvision pytorch-cuda=11.6 -c pytorch -c nvidia
 ```
 
-if the follwoing error  occurs:
+if the follwoing error occurs:
+
 ```
 :ImportError: libtiff.so.5: cannot open shared object file: No such file or directory
 ```
+
 you can resolve it via:
 
 ```
@@ -64,7 +85,8 @@ conda install -c anaconda libtiff==4.4.0
 
 ### Quick start
 
-Affinity-vae has a running script (`run.py`)that allows you to configure and run the code. You can look at the avaible configuration options by running:
+Affinity-vae has a running script (`run.py`)that allows you to configure and run
+the code. You can look at the avaible configuration options by running:
 
 ```
 python run.py --help
@@ -201,42 +223,54 @@ Options:
   --help                          Show this message and exit.
 ```
 
-Note that setting ```-g/--gamma``` to ```0``` and ```-pd/--pose_dims``` to ```0``` will run a vanilla beta-VAE.
+Note that setting `-g/--gamma` to `0` and `-pd/--pose_dims` to `0` will run a
+vanilla beta-VAE.
 
 ### Quickstart
 
 #### Configuring from the command line
 
-
 You can run on example data with the following command:
 
 ```
 python affinity-vae/run.py -d data/subtomo_files --split 20 --epochs 10 -ba 128 -lr 0.001 -de 4 -ch 64 -ld 8 -pd 3 --beta 1 --gamma 2 --limit 1000 --freq_all 5 --vis_all --dynamic
 ```
-where the **subtomo_files** is a directory with a number of `.mcr` proteine image files named with the protein keyword such as (`1BXN_m0_156_Th0.mrc`,`5MRC_m8_1347_Th0.mrc`, etc). The **subtomo_files** directory should also have be a `classes.csv` file with a list of the protein names and keywords to be considered (`1BXN`, `5MRC`, etc.) and a `affinity_scores.csv` matrix with the initial values for the proteins named in the `classes.csv`.
+
+where the **subtomo_files** is a directory with a number of `.mcr` proteine
+image files named with the protein keyword such as
+(`1BXN_m0_156_Th0.mrc`,`5MRC_m8_1347_Th0.mrc`, etc). The **subtomo_files**
+directory should also have be a `classes.csv` file with a list of the protein
+names and keywords to be considered (`1BXN`, `5MRC`, etc.) and a
+`affinity_scores.csv` matrix with the initial values for the proteins named in
+the `classes.csv`.
 
 #### Using a config submission file
 
-You can also run the code using a submission config file (you can find an example with default values
-on `configs/avae-test-config.yml`). For example, you can run the following command:
+You can also run the code using a submission config file (you can find an
+example with default values on `configs/avae-test-config.yml`). For example, you
+can run the following command:
 
 ```
 python affinity-vae/run.py --config_file affinity-vae/configs/avae-test-config.yml
 ```
 
-You can also use a mix of config file and command line arguments. For example, you can run the following command:
+You can also use a mix of config file and command line arguments. For example,
+you can run the following command:
 
 ```
 python affinity-vae/run.py --config_file affinity-vae/configs/avae-test-config.yml --epochs 10 --affinity /path/to/different_affinity.csv
 ```
 
-this will rewrite the values for the epochs and affinity path in the config file.
-
-At the end of the run, the code will save the final config file used for the run in the working directory. This will
-account for any changes made to the config file from the command line. Running the code again with that config file will reproduce the results.
+this will rewrite the values for the epochs and affinity path in the config
+file.
 
+At the end of the run, the code will save the final config file used for the run
+in the working directory. This will account for any changes made to the config
+file from the command line. Running the code again with that config file will
+reproduce the results.
 
-In the tools folder you can find notebooks which will assist you in creating the input files for Affinity-VAE or analyse teh output of the model.
+In the tools folder you can find notebooks which will assist you in creating the
+input files for Affinity-VAE or analyse teh output of the model.
 
 #### Considerations
 

configs/avae-create_subtomo_test_config.yml

@@ -10,7 +10,6 @@
 #  Not implemented yet : can apply crop after rotation
 #  Not Implemented yet: gaussian blur
 
-
 #### Data parameters
 input_path: /Users/mfamili/work/test_affinity_merge/test_create_subtomo_avae
 annot_path: /Users/mfamili/work/test_affinity_merge/test_create_subtomo_avae
@@ -20,8 +19,6 @@ output_path: /Users/mfamili/work/test_affinity_merge/test_create_subtomo_avae/su
 datatype: mrc
 vox_size: [32, 32, 32]
 
-
-
 ### Filters
 bandpass: False
 low_freq: 0
@@ -31,7 +28,6 @@ normalise: True
 add_noise: True
 noise_int: 3
 
-
 #### augmentation
 augment: 3
 aug_th_min: -20