Merge remote-tracking branch 'origin/main' into compile_fix

.pre-commit-config.yaml

@@ -40,10 +40,33 @@ repos:
 
   # python docstring formatting
   - repo: https://github.com/myint/docformatter
-    rev: v1.5.1
+    rev: v1.7.4
     hooks:
       - id: docformatter
-        args: [--in-place, --wrap-summaries=99, --wrap-descriptions=99]
+        args:
+          [
+            --in-place,
+            --wrap-summaries=99,
+            --wrap-descriptions=99,
+            --style=sphinx,
+            --black,
+          ]
+
+  # python docstring coverage checking
+  - repo: https://github.com/econchick/interrogate
+    rev: 1.5.0 # or master if you're bold
+    hooks:
+      - id: interrogate
+        args:
+          [
+            --verbose,
+            --fail-under=80,
+            --ignore-init-module,
+            --ignore-init-method,
+            --ignore-module,
+            --ignore-nested-functions,
+            -vv,
+          ]
 
   # python check (PEP8), programming errors and code complexity
   - repo: https://github.com/PyCQA/flake8
@@ -53,10 +76,11 @@ repos:
         args:
           [
             "--extend-ignore",
-            "E203,E402,E501,F401,F841",
+            "E203,E402,E501,F401,F841,RST2,RST301",
             "--exclude",
             "logs/*,data/*",
           ]
+        additional_dependencies: [flake8-rst-docstrings==0.3.0]
 
   # python security linter
   - repo: https://github.com/PyCQA/bandit

configs/callbacks/default.yaml

@@ -1,8 +1,8 @@
 defaults:
-  - model_checkpoint.yaml
-  - early_stopping.yaml
-  - model_summary.yaml
-  - rich_progress_bar.yaml
+  - model_checkpoint
+  - early_stopping
+  - model_summary
+  - rich_progress_bar
   - _self_
 
 model_checkpoint:

configs/debug/fdr.yaml

@@ -3,7 +3,7 @@
 # runs 1 train, 1 validation and 1 test step
 
 defaults:
-  - default.yaml
+  - default
 
 trainer:
   fast_dev_run: true

configs/debug/limit.yaml

@@ -3,7 +3,7 @@
 # uses only 1% of the training data and 5% of validation/test data
 
 defaults:
-  - default.yaml
+  - default
 
 trainer:
   max_epochs: 3

configs/debug/overfit.yaml

@@ -3,7 +3,7 @@
 # overfits to 3 batches
 
 defaults:
-  - default.yaml
+  - default
 
 trainer:
   max_epochs: 20

configs/debug/profiler.yaml

@@ -3,7 +3,7 @@
 # runs with execution time profiling
 
 defaults:
-  - default.yaml
+  - default
 
 trainer:
   max_epochs: 1

configs/eval.yaml

@@ -2,13 +2,13 @@
 
 defaults:
   - _self_
-  - data: mnist.yaml # choose datamodule with `test_dataloader()` for evaluation
-  - model: mnist.yaml
+  - data: mnist # choose datamodule with `test_dataloader()` for evaluation
+  - model: mnist
   - logger: null
-  - trainer: default.yaml
-  - paths: default.yaml
-  - extras: default.yaml
-  - hydra: default.yaml
+  - trainer: default
+  - paths: default
+  - extras: default
+  - hydra: default
 
 task_name: "eval"
 

configs/experiment/example.yaml

@@ -4,10 +4,10 @@
 # python train.py experiment=example
 
 defaults:
-  - override /data: mnist.yaml
-  - override /model: mnist.yaml
-  - override /callbacks: default.yaml
-  - override /trainer: default.yaml
+  - override /data: mnist
+  - override /model: mnist
+  - override /callbacks: default
+  - override /trainer: default
 
 # all parameters below will be merged with parameters from default configurations set above
 # this allows you to overwrite only specified parameters

configs/hydra/default.yaml

@@ -11,3 +11,9 @@ run:
 sweep:
   dir: ${paths.log_dir}/${task_name}/multiruns/${now:%Y-%m-%d}_${now:%H-%M-%S}
   subdir: ${hydra.job.num}
+
+job_logging:
+  handlers:
+    file:
+      # Incorporates fix from https://github.com/facebookresearch/hydra/pull/2242
+      filename: ${hydra.runtime.output_dir}/${hydra.job.name}.log

configs/logger/many_loggers.yaml

@@ -1,9 +1,9 @@
 # train with many loggers at once
 
 defaults:
-  # - comet.yaml
-  - csv.yaml
-  # - mlflow.yaml
-  # - neptune.yaml
-  - tensorboard.yaml
-  - wandb.yaml
+  # - comet
+  - csv
+  # - mlflow
+  # - neptune
+  - tensorboard
+  - wandb

configs/train.yaml

@@ -4,14 +4,14 @@
 # order of defaults determines the order in which configs override each other
 defaults:
   - _self_
-  - data: mnist.yaml
-  - model: mnist.yaml
-  - callbacks: default.yaml
+  - data: mnist
+  - model: mnist
+  - callbacks: default
   - logger: null # set logger here or use command line (e.g. `python train.py logger=tensorboard`)
-  - trainer: default.yaml
-  - paths: default.yaml
-  - extras: default.yaml
-  - hydra: default.yaml
+  - trainer: default
+  - paths: default
+  - extras: default
+  - hydra: default
 
   # experiment configs allow for version control of specific hyperparameters
   # e.g. best hyperparameters for given model and datamodule
@@ -22,7 +22,7 @@ defaults:
 
   # optional local config for machine/user specific settings
   # it's optional since it doesn't need to exist and is excluded from version control
-  - optional local: default.yaml
+  - optional local: default
 
   # debugging config (enable through command line, e.g. `python train.py debug=default)
   - debug: null

configs/trainer/cpu.yaml

@@ -1,5 +1,5 @@
 defaults:
-  - default.yaml
+  - default
 
 accelerator: cpu
 devices: 1

configs/trainer/ddp.yaml

@@ -1,5 +1,5 @@
 defaults:
-  - default.yaml
+  - default
 
 strategy: ddp
 

configs/trainer/ddp_sim.yaml

@@ -1,5 +1,5 @@
 defaults:
-  - default.yaml
+  - default
 
 # simulate DDP on CPU, useful for debugging
 accelerator: cpu

configs/trainer/gpu.yaml

@@ -1,5 +1,5 @@
 defaults:
-  - default.yaml
+  - default
 
 accelerator: gpu
 devices: 1

configs/trainer/mps.yaml

@@ -1,5 +1,5 @@
 defaults:
-  - default.yaml
+  - default
 
 accelerator: mps
 devices: 1

environment.yaml

@@ -42,4 +42,4 @@ dependencies:
   - pip:
       - hydra-optuna-sweeper
       - hydra-colorlog
-      - pyrootutils
+      - rootutils

requirements.txt

@@ -18,7 +18,7 @@ hydra-optuna-sweeper==1.2.0
 # aim>=3.16.2  # no lower than 3.16.2, see https://github.com/aimhubio/aim/issues/2550
 
 # --------- others --------- #
-pyrootutils     # standardizing the project root setup
+rootutils       # standardizing the project root setup
 pre-commit      # hooks for applying linters on commit
 rich            # beautiful text formatting in terminal
 pytest          # tests