CLI revamp (#184)

* Overhaul runner

* Update linting to only happen once

* Fix linting error

* Specify utf-8 encoding

* Specify utf-8 encoding only for default config

* Skip weights tests for now

* Update skipping API test

* Revert accidental max_epochs change

* msg -> reason for pytest.mark.skip

* Wout's suggestions and more tests

* Remove encoding

* Specify device type when weight loading

* Fix lint

* Capture init params and figure out device automagically

* Add runner tests

* Fix bug and limit saved models

* WIP

* Support old weights too

* Remove every_n_train_steps from checkpoint

* Implementation done. Need to update tests

* Update tests

* add -h

* Add auto screenshot generation

* Add screenshots workflow [screenshots]

* Add manual dispatch

* Added image

* Updated instructions [screenshots]

* Update screenshot workflow

* Fix bug and screenshot uploads

* Restirct workflow

* fix ref

* Generate new screengrabs with rich-codex

* increase timeout

* bump changelog and increase timeout

* Generate new screengrabs with rich-codex

* Add more tests

* Add option for calculating precision during training

* Restrict depthcharge version

* Log scalars instead of tensors

* Fix typo

* Fix issue Wout found

* Write to stdout instead of stderr

* Minor refactoring

* Separate logger and model initialization

* Generate new screengrabs with rich-codex

* Generate new screengrabs with rich-codex

* Fix test formatting

* Fix edge case

---------

Co-authored-by: melihyilmaz <yilmazmelih97@gmail.com>
Co-authored-by: github-actions[bot] <github-actions[bot]@users.noreply.github.com>
Co-authored-by: Wout Bittremieux <wout@bittremieux.be>

.github/workflows/screenshots.yml

@@ -0,0 +1,29 @@
+name: Screenshots with rich-codex
+on:
+ pull_request:
+ paths:
+ - "docs/*.md"
+ - "casanovo/casanovo.py"
+ workflow_dispatch:
+
+jobs:
+ rich_codex:
+ runs-on: ubuntu-latest
+ steps:
+ - name: Check out the repo
+ uses: actions/checkout@v3
+ with:
+ ref: ${{ github.head_ref }}
+
+ - name: Set up Python
+ uses: actions/setup-python@v3
+
+ - name: Install your custom tools
+ run: pip install .
+
+ - name: Generate terminal images with rich-codex
+ uses: ewels/rich-codex@v1
+ with:
+ timeout: 10
+ commit_changes: "true"
+ clean_img_paths: docs/images/*.svg

CHANGELOG.md

@@ -6,8 +6,21 @@ The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/),
 
 ## [Unreleased]
 
+### Changed
+
+- The CLI has been overhauled to use subcommands.
+- Upgraded to Lightning >=2.0
+- Checkpointing is now configured to save the top-k models instead of all.
+
+### Fixed
+
+- Casanovo now runs on CPU and can passes all tests.
+
 ### Added
 
+- Checkpoints now include model parameters, allowing for mismatches with the provided configuration file.
+- `accelerator` parameter now controls the accelerator (CPU, GPU, etc) that is used.
+- `devices` parameter controls the number of accelerators used.
 - `every_n_train_steps` parameter now controls the frequency of both validation epochs and model checkpointing during training.
 
 ### Changed