solving some reprod issues, some wip,

cantinilab · Nov 27, 2024 · 53e09ea · 53e09ea
1 parent 3aadbbe
commit 53e09ea
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diff --git a/.gitignore b/.gitignore
@@ -183,3 +183,5 @@ file.txt
 tests/data/step_0__predict_part_0_0.h5ad
 data/human_dcm_hcm_nf/
 data/geneformertest.csv
+clf_omni.pkl
+metrics__step0.json
diff --git a/Makefile b/Makefile
@@ -71,6 +71,7 @@ release:          ## Create a new tag for release.
 	@read -p "Version? (provide the next x.y.z semver) : " TAG
 	@echo "$${TAG}" > scprint/VERSION
 	@sed -i 's/^version = .*/version = "'$${TAG}'"/' pyproject.toml
+	@sed -i 's/__version__ = .*/__version__ = "'$${TAG}'"/' scprint/__init__.py
 	@$(ENV_PREFIX)gitchangelog > HISTORY.md
 	@git add scprint/VERSION HISTORY.md pyproject.toml
 	@git commit -m "release: version $${TAG} 🚀"

diff --git a/README.md b/README.md
@@ -80,11 +80,11 @@ To use scPRINT, you will need to use [lamin.ai](https://lamin.ai/). This is need
 To start you will need to do:
 
 ```bash
-conda create -n <env-name> python==3.10 #scprint might work with python >3.10, but it is not tested
+uv venv -n <env-name> python==3.10 #scprint might work with python >3.10, but it is not tested
 #one of
-pip install scprint # OR
-pip install scprint[dev] # for the dev dependencies (building etc..) OR
-pip install scprint[flash] # to use flashattention2 with triton: only if you have a compatible gpu (e.g. not available for apple GPUs for now, see https://github.com/triton-lang/triton?tab=readme-ov-file#compatibility)
+uv pip install scprint # OR
+uv pip install scprint[dev] # for the dev dependencies (building etc..) OR
+uv pip install scprint[flash] # to use flashattention2 with triton: only if you have a compatible gpu (e.g. not available for apple GPUs for now, see https://github.com/triton-lang/triton?tab=readme-ov-file#compatibility)
 #OR pip install scPRINT[dev,flash]
 
 lamin init --storage ./testdb --name test --schema bionty

diff --git a/config.yaml b/config.yaml
@@ -8,70 +8,70 @@ trainer:
   precision: 16
   logger: false
   callbacks:
-  - class_path: scprint.trainer.TrainingMode
-    init_args:
-      do_denoise: true
-      noise:
-      - 0.3
-      do_cce: true
-      cce_sim: 0.5
-      do_ecs: true
-      ecs_threshold: 0.3
-      ecs_scale: 1.0
-      do_mvc: false
-      do_adv_cls: false
-      do_next_tp: false
-      class_scale: 1.0
-      mask_ratio:
-      - 0.15
-      - 0.3
-      log_grad: false
-  - class_path: lightning.pytorch.callbacks.StochasticWeightAveraging
-    init_args:
-      swa_lrs: 0.01
-      swa_epoch_start: 0.8
-      annealing_epochs: 10
-      annealing_strategy: cos
-      avg_fn: null
-      device: cpu
-  - class_path: lightning.pytorch.callbacks.ModelCheckpoint
-    init_args:
-      dirpath: null
-      filename: null
-      monitor: val_loss
-      verbose: false
-      save_last: null
-      save_top_k: -1
-      save_weights_only: false
-      mode: min
-      auto_insert_metric_name: true
-      every_n_train_steps: null
-      train_time_interval: null
-      every_n_epochs: null
-      save_on_train_epoch_end: null
-  - class_path: lightning.pytorch.callbacks.EarlyStopping
-    init_args:
-      monitor: val_loss
-      min_delta: 0.0
-      patience: 10
-      verbose: false
-      mode: min
-      strict: true
-      check_finite: true
-      stopping_threshold: null
-      divergence_threshold: null
-      check_on_train_epoch_end: null
-      log_rank_zero_only: false
-  - class_path: lightning.pytorch.callbacks.LearningRateMonitor
-    init_args:
-      logging_interval: step
-      log_momentum: false
+    - class_path: scprint.trainer.TrainingMode
+      init_args:
+        do_denoise: true
+        noise:
+          - 0.3
+        do_cce: true
+        cce_sim: 0.5
+        do_ecs: true
+        ecs_threshold: 0.3
+        ecs_scale: 1.0
+        do_mvc: false
+        do_adv_cls: false
+        do_next_tp: false
+        class_scale: 1.0
+        mask_ratio:
+          - 0.15
+          - 0.3
+        log_grad: false
+    - class_path: lightning.pytorch.callbacks.StochasticWeightAveraging
+      init_args:
+        swa_lrs: 0.01
+        swa_epoch_start: 0.8
+        annealing_epochs: 10
+        annealing_strategy: cos
+        avg_fn: null
+        device: cpu
+    - class_path: lightning.pytorch.callbacks.ModelCheckpoint
+      init_args:
+        dirpath: null
+        filename: null
+        monitor: val_loss
+        verbose: false
+        save_last: null
+        save_top_k: -1
+        save_weights_only: false
+        mode: min
+        auto_insert_metric_name: true
+        every_n_train_steps: null
+        train_time_interval: null
+        every_n_epochs: null
+        save_on_train_epoch_end: null
+    - class_path: lightning.pytorch.callbacks.EarlyStopping
+      init_args:
+        monitor: val_loss
+        min_delta: 0.0
+        patience: 10
+        verbose: false
+        mode: min
+        strict: true
+        check_finite: true
+        stopping_threshold: null
+        divergence_threshold: null
+        check_on_train_epoch_end: null
+        log_rank_zero_only: false
+    - class_path: lightning.pytorch.callbacks.LearningRateMonitor
+      init_args:
+        logging_interval: step
+        log_momentum: false
   fast_dev_run: false
   max_epochs: null
   min_epochs: null
   max_steps: -1
   min_steps: null
-  max_time: '{''hours'': 12}'
+  max_time: "{'hours': 12}"
   limit_train_batches: null
   limit_val_batches: null
   limit_test_batches: null
@@ -112,10 +112,10 @@ model:
   n_input_bins: 0
   mvc_decoder: inner product
   pred_embedding:
-  - cell_type_ontology_term_id
-  - disease_ontology_term_id
-  - self_reported_ethnicity_ontology_term_id
-  - sex_ontology_term_id
+    - cell_type_ontology_term_id
+    - disease_ontology_term_id
+    - self_reported_ethnicity_ontology_term_id
+    - sex_ontology_term_id
   cell_emb_style: cls
   lr: 0.001
   residual_in_fp32: true
@@ -128,47 +128,47 @@ model:
   fused_mlp: false
   fused_bias_fc: false
   sequence_parallel: false
-  drop_path_rate: 0.02
-  weight_init: ''
+  drop_path_rate: 0
+  weight_init: ""
 data:
   mdataset: null
   collection_name: preprocessed dataset
   organisms:
-  - NCBITaxon:9606
+    - NCBITaxon:9606
   weight_scaler: 30
   label_to_weight:
-  - cell_type_ontology_term_id
-  - disease_ontology_term_id
-  - assay_ontology_term_id
-  - self_reported_ethnicity_ontology_term_id
-  - sex_ontology_term_id
-  - organism_ontology_term_id
+    - cell_type_ontology_term_id
+    - disease_ontology_term_id
+    - assay_ontology_term_id
+    - self_reported_ethnicity_ontology_term_id
+    - sex_ontology_term_id
+    - organism_ontology_term_id
   label_to_pred:
-  - cell_type_ontology_term_id
-  - disease_ontology_term_id
-  - assay_ontology_term_id
-  - self_reported_ethnicity_ontology_term_id
-  - sex_ontology_term_id
-  - organism_ontology_term_id
+    - cell_type_ontology_term_id
+    - disease_ontology_term_id
+    - assay_ontology_term_id
+    - self_reported_ethnicity_ontology_term_id
+    - sex_ontology_term_id
+    - organism_ontology_term_id
   validation_split: 0.2
   test_split: 0.0
   use_default_col: true
   all_clss:
-  - cell_type_ontology_term_id
-  - disease_ontology_term_id
-  - assay_ontology_term_id
-  - self_reported_ethnicity_ontology_term_id
-  - sex_ontology_term_id
-  - organism_ontology_term_id
-  - heat_diff
-  - total_counts
-  - nnz
-  - dpt_group
+    - cell_type_ontology_term_id
+    - disease_ontology_term_id
+    - assay_ontology_term_id
+    - self_reported_ethnicity_ontology_term_id
+    - sex_ontology_term_id
+    - organism_ontology_term_id
+    - heat_diff
+    - total_counts
+    - nnz
+    - dpt_group
   hierarchical_labels:
-  - cell_type_ontology_term_id
-  - disease_ontology_term_id
-  - assay_ontology_term_id
-  - self_reported_ethnicity_ontology_term_id
+    - cell_type_ontology_term_id
+    - disease_ontology_term_id
+    - assay_ontology_term_id
+    - self_reported_ethnicity_ontology_term_id
   how: most expr
   organism_name: organism_ontology_term_id
   max_len: 1000
@@ -188,7 +188,7 @@ data:
   generator: null
   prefetch_factor: null
   persistent_workers: false
-  pin_memory_device: ''
+  pin_memory_device: ""
 set_float32_matmul_precision: true
 project: scprint_test
 ckpt_path: null