topcup 1.0.1__tar.gz

topcup-1.0.1/LICENSE.md

@@ -0,0 +1,41 @@
+# Legal
+
+## License for the octopi package
+
+This package is licensed under the MIT License:
+
+```
+MIT License
+
+Copyright (c) 2025 Chan Zuckerberg Initiative
+
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in all
+copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+SOFTWARE.
+```
+
+## License Notice for Dependencies
+
+```
+This repository is licensed under the MIT License; however, it relies on certain third-party dependencies that are licensed under the GNU General Public License (GPL). Specifically:
+
+- monai is licensed under the Apache License 2.0.
+- pytorch-lightning is licensed under the Apache License 2.0.
+
+All dependencies use permissive open-source licenses that are compatible with this project's MIT License. No GPL or other copyleft licensed dependencies are included.
+For specific licensing information about any dependency, please refer to the respective package documentation or repository.
+```

topcup-1.0.1/PKG-INFO

@@ -0,0 +1,301 @@
+Metadata-Version: 2.4
+Name: topcup
+Version: 1.0.1
+Summary: An implementation of 2024-2025 Kaggle/CZI cryoET ML challenge winning models
+Author-email: Zhuowen Zhao <kevin.zhao@biohub.org>, Christof Henkel <chenkel@nvidia.com>, Eugene Khvedchenya <ekhvedchenia@nvidia.com>
+Project-URL: Homepage, https://github.com/czimaginginstitute/czii_cryoet_challenge_models
+Requires-Python: >=3.10
+Description-Content-Type: text/markdown
+License-File: LICENSE.md
+Requires-Dist: copick
+Requires-Dist: scikit-learn
+Requires-Dist: zarr==2.18.2
+Requires-Dist: numcodecs==0.11.0
+Requires-Dist: pandas
+Requires-Dist: einops
+Requires-Dist: albumentations==1.4.21
+Requires-Dist: opencv-python==4.12.0.88
+Requires-Dist: timm==1.0.11
+Requires-Dist: torch==2.4.*
+Requires-Dist: torchvision==0.19.*
+Requires-Dist: pytorch-lightning==2.4.*
+Requires-Dist: monai==1.5.0
+Requires-Dist: mrcfile
+Dynamic: license-file
+
+#  TopCUP: Top CryoET U-Net Picker 🏆🏆🏆
+The re-implementation of 1st winning team's solution [kaggle-cryoet-1st-place-segmentation](https://github.com/ChristofHenkel/kaggle-cryoet-1st-place-segmentation/tree/main) in pytorch-lightning and copick.
+
+
+## Performance
+We are able to train 3 models (resnet34 backbones) with 6, 12, and 24 tomograms respectively, and achieved an esenmble score of 0.774. This is comparable to the original submission of the 1st place [kaggle-cryoet-leader-board](https://www.kaggle.com/competitions/czii-cryo-et-object-identification/leaderboard).
+<p align="center">
+  <img src="assets/scores.png" alt="F4 score of each protein complex using different training set sizes">
+</p>
+
+
+
+## Installation
+```
+pip install git+https://github.com/czimaginginstitute/czii_cryoet_mlchallenge_winning_models.git
+```
+
+Or cd into the root folder, then 
+```
+pip install -e .
+```
+
+## 🚀 Quickstart  
+You can explore and train TopCUP models using the provided example notebooks:  
+- [Quickstart notebook](https://github.com/czimaginginstitute/czii_cryoet_mlchallenge_winning_models/blob/main/notebooks/Quickstart_TopCUP.ipynb): Run inference with pretrained TopCUP models.  
+- [Training notebook](https://github.com/czimaginginstitute/czii_cryoet_mlchallenge_winning_models/blob/main/notebooks/Tutorial_training_TopCUP.ipynb): Learn how to train or fine-tune a TopCUP model using your own tomograms.  
+
+
+## Copick configuration file
+The copick data ingestion can automatically populate many important internal variables from the config file. Especially, the metrics for the training and evaluation process, such as `class_loss_weight`, `score_threshold`, and `score_weight` are stored under the metadata key in the configuration file. 
+
+- `class_loss_weight`: weighting each class in the DenseCrossEntrope loss
+- `score_threshold`: white filter picks per class above the value from the final probability--reduce false positives 
+- `score_weight`: weighting each class in the F beta score 
+
+An example of copick config file is shown below:
+```
+{
+    "name": "Phatom Dataset",
+    "description": "CZII ML Challenge Training dataset",
+    "version": "1.0.1",
+    "pickable_objects": [
+        {
+            "name": "apo-ferritin",
+            "is_particle": true,
+            "pdb_id": "4V1W",
+            "label": 1,
+            "color": [  0, 117, 220, 255],
+            "radius": 60,
+            "map_threshold": 0.0418,
+            "metadata": {
+                "score_weight": 1,
+                "score_threshold": 0.16,
+                "class_loss_weight": 256
+            }
+        },
+        {
+            "name": "beta-amylase",
+            "is_particle": true,
+            "pdb_id": "1FA2",
+            "label": 2,
+            "color": [153,  63,   0, 255],
+            "radius": 65,
+            "map_threshold": 0.035,
+            "metadata": {
+                "score_weight": 0,
+                "score_threshold": 0.25,
+                "class_loss_weight": 256
+            }
+        },
+        {
+            "name": "beta-galactosidase",
+            "is_particle": true,
+            "pdb_id": "6X1Q",
+            "label": 3,
+            "color": [ 76,   0,  92, 255],
+            "radius": 90,
+            "map_threshold": 0.0578,
+            "metadata": {
+                "score_weight": 2,
+                "score_threshold": 0.13,
+                "class_loss_weight": 256
+            }
+        },
+        {
+            "name": "ribosome",
+            "is_particle": true,
+            "pdb_id": "6EK0",
+            "label": 4,
+            "color": [  0,  92,  49, 255],
+            "radius": 150,
+            "map_threshold": 0.0374,
+            "metadata": {
+                "score_weight": 1,
+                "score_threshold": 0.19,
+                "class_loss_weight": 256
+            }
+        },
+        {
+            "name": "thyroglobulin",
+            "is_particle": true,
+            "pdb_id": "6SCJ",
+            "label": 5,
+            "color": [ 43, 206,  72, 255],
+            "radius": 130,
+            "map_threshold": 0.0278,
+            "metadata": {
+                "score_weight": 2,
+                "score_threshold": 0.18,
+                "class_loss_weight": 256
+            }
+        },
+        {
+            "name": "virus-like-particle",
+            "is_particle": true,
+            "label": 6,
+            "color": [255, 204, 153, 255],
+            "radius": 135,
+            "map_threshold": 0.201,
+            "metadata": {
+                "score_weight": 1,
+                "score_threshold": 0.5,
+                "class_loss_weight": 256
+            }
+        }
+    ],
+    "config_type": "filesystem",
+    "overlay_root": "local:///PATH/TO/EXTRACTED/PROJECT/",
+    "static_root": "local:///PATH/TO/EXTRACTED/PROJECT/"
+}
+```
+
+## Commands
+After installation, use the command `topcup --help` to show all the possible subcomamnds:
+```
+Usage: topcup [OPTIONS] COMMAND [ARGS]...
+
+  topcup: a top crypet u-net picker
+
+Options:
+  -v, --verbose  Increase verbosity (-v, -vv).
+  --version      Show the version and exit.
+  -h, --help     Show this message and exit.
+
+Commands:
+  inference
+  train
+  score
+```
+
+### Training from scratch
+Use `topcup train --help` to see all the options for training. The code support loading data via copick. An example training command is below.
+```
+topcup train \
+    --copick_config COPICK_CONFIG_FILE \
+    --train_run_names TS_6_4,TS_6_6,TS_69_2,TS_73_6,TS_86_3,TS_99_9 \
+    --val_run_names TS_5_4 \
+    --tomo_type denoised \
+    --user_id COPICK_USER_ID \
+    --pixelsize 10 \  
+    --batch_size 16 \
+    --n_aug 1112 \
+    --output_dir OUTPUT_PATH \
+    --logger_version 1 \
+    --epochs 100   
+```
+
+### Re-training from a checkpoint for the same dataset
+```
+topcup train \
+    --copick_config COPICK_CONFIG_FILE \
+    --train_run_names TS_6_4,TS_6_6,TS_69_2,TS_73_6,TS_86_3,TS_99_9 \
+    --val_run_names TS_5_4  \
+    --tomo_type denoised \
+    --user_id COPICK_USER_ID \
+    --pixelsize 10 \  
+    --batch_size 16 \
+    --n_aug 1112 \
+    --output_dir OUTPUT_PATH \
+    --logger_version 1 \
+    --epochs 100 \
+    --pretrained_weight CHECKPOINT_PATH   
+```
+
+### *Subset transfer learning: re-training from a checkpoint for a different dataset 
+**Subset transfer learning** involves loading a checkpoint from a pretrained model and fine-tuning it on a new dataset that includes only a subset of the original classes. To do this correctly, it’s important to know which classes and the corresponding `channel_id` the original model was trained on. This information can be accessed by loading the checkpoint and inspecting the `model.description` attribute. The `copick_config` used for fine-tuning should include the same pickable objects as the original training setup, with updated class weights and thresholds as needed for the new task.
+
+```
+>>> from czii_cryoet_models.model import SegNet
+>>> model = SegNet.load_from_checkpoint('/hpc/projects/group.czii/kevin.zhao/ml_challenge/winning_models/czii_cryoet_mlchallenge_models/output_test/checkpoints/best_model-v6.ckpt')
+>>> print(model.description)
+SegNet model predicting 6 classes
+
+Class details:
+{
+  "apo-ferritin": {
+    "channel_id": 0,
+    "radius": 60.0,
+    "score_threshold": 0.16,
+    "score_weight": 1
+  },
+  "beta-amylase": {
+    "channel_id": 1,
+    "radius": 65.0,
+    "score_threshold": 0.25,
+    "score_weight": 0
+  },
+  "beta-galactosidase": {
+    "channel_id": 2,
+    "radius": 90.0,
+    "score_threshold": 0.13,
+    "score_weight": 2
+  },
+  "ribosome": {
+    "channel_id": 3,
+    "radius": 150.0,
+    "score_threshold": 0.19,
+    "score_weight": 1
+  },
+  "thyroglobulin": {
+    "channel_id": 4,
+    "radius": 130.0,
+    "score_threshold": 0.18,
+    "score_weight": 2
+  },
+  "virus-like-particle": {
+    "channel_id": 5,
+    "radius": 135.0,
+    "score_threshold": 0.5,
+    "score_weight": 1
+  }
+}
+```
+
+
+### Inference
+Use command `topcup inference --help` to see all the options for the inference pipeline. An example command for inference with PyTorch checkpoints (a single checkpoint file path or multiple folder paths, each containing mutiple checkpoints) that supports pattern matching. 
+
+```
+topcup inference \
+    --copick_config copick_config.json \
+    --run_names TS_100_4,TS_100_6,TS_100_7,TS_100_9 \
+    --tomo_type denoised \
+    --user_id COPICK_USER_ID \
+    --pretrained_weights FOLDER_PATH1/checkpoints/,FOLDER_PATH2/checkpoints/,FOLDER_PATH3/checkpoints/ \
+    --batch_size 16 \
+    --output_dir OUTPUT_PATH \
+    --pattern *v1.ckpt 
+```
+
+### Score calculation
+Use command 'topcup score --help' to see all the options for calculating F-beta score for the predictions:
+```
+Usage: topcup score [OPTIONS]
+
+Options:
+  -c, --copick_config FILE  copick config file path  [required]
+  -g, --gt FILE             Ground truth picks csv file path  [required]
+  -s, --submission FILE     Submission picks csv file path  [required]
+  -h, --help                Show this message and exit.
+```
+
+
+## 📚 Documentation
+
+Coming soon.
+
+## 🤝 Contributor covenant code of conduct
+
+This project adheres to the Contributor Covenant code of conduct. By participating, you are expected to uphold this code. Please report unacceptable behavior to opensource@chanzuckerberg.com.
+
+Responsible Use: We are committed to advancing the responsible development and use of artificial intelligence. Please follow our [Acceptable Use Policy](https://virtualcellmodels.cziscience.com/acceptable-use-policy) when engaging with the model.
+
+## 🔒 Security
+
+If you believe you have found a security issue, please responsibly disclose by contacting us at security@chanzuckerberg.com.

topcup-1.0.1/README.md

@@ -0,0 +1,276 @@
+#  TopCUP: Top CryoET U-Net Picker 🏆🏆🏆
+The re-implementation of 1st winning team's solution [kaggle-cryoet-1st-place-segmentation](https://github.com/ChristofHenkel/kaggle-cryoet-1st-place-segmentation/tree/main) in pytorch-lightning and copick.
+
+
+## Performance
+We are able to train 3 models (resnet34 backbones) with 6, 12, and 24 tomograms respectively, and achieved an esenmble score of 0.774. This is comparable to the original submission of the 1st place [kaggle-cryoet-leader-board](https://www.kaggle.com/competitions/czii-cryo-et-object-identification/leaderboard).
+<p align="center">
+  <img src="assets/scores.png" alt="F4 score of each protein complex using different training set sizes">
+</p>
+
+
+
+## Installation
+```
+pip install git+https://github.com/czimaginginstitute/czii_cryoet_mlchallenge_winning_models.git
+```
+
+Or cd into the root folder, then 
+```
+pip install -e .
+```
+
+## 🚀 Quickstart  
+You can explore and train TopCUP models using the provided example notebooks:  
+- [Quickstart notebook](https://github.com/czimaginginstitute/czii_cryoet_mlchallenge_winning_models/blob/main/notebooks/Quickstart_TopCUP.ipynb): Run inference with pretrained TopCUP models.  
+- [Training notebook](https://github.com/czimaginginstitute/czii_cryoet_mlchallenge_winning_models/blob/main/notebooks/Tutorial_training_TopCUP.ipynb): Learn how to train or fine-tune a TopCUP model using your own tomograms.  
+
+
+## Copick configuration file
+The copick data ingestion can automatically populate many important internal variables from the config file. Especially, the metrics for the training and evaluation process, such as `class_loss_weight`, `score_threshold`, and `score_weight` are stored under the metadata key in the configuration file. 
+
+- `class_loss_weight`: weighting each class in the DenseCrossEntrope loss
+- `score_threshold`: white filter picks per class above the value from the final probability--reduce false positives 
+- `score_weight`: weighting each class in the F beta score 
+
+An example of copick config file is shown below:
+```
+{
+    "name": "Phatom Dataset",
+    "description": "CZII ML Challenge Training dataset",
+    "version": "1.0.1",
+    "pickable_objects": [
+        {
+            "name": "apo-ferritin",
+            "is_particle": true,
+            "pdb_id": "4V1W",
+            "label": 1,
+            "color": [  0, 117, 220, 255],
+            "radius": 60,
+            "map_threshold": 0.0418,
+            "metadata": {
+                "score_weight": 1,
+                "score_threshold": 0.16,
+                "class_loss_weight": 256
+            }
+        },
+        {
+            "name": "beta-amylase",
+            "is_particle": true,
+            "pdb_id": "1FA2",
+            "label": 2,
+            "color": [153,  63,   0, 255],
+            "radius": 65,
+            "map_threshold": 0.035,
+            "metadata": {
+                "score_weight": 0,
+                "score_threshold": 0.25,
+                "class_loss_weight": 256
+            }
+        },
+        {
+            "name": "beta-galactosidase",
+            "is_particle": true,
+            "pdb_id": "6X1Q",
+            "label": 3,
+            "color": [ 76,   0,  92, 255],
+            "radius": 90,
+            "map_threshold": 0.0578,
+            "metadata": {
+                "score_weight": 2,
+                "score_threshold": 0.13,
+                "class_loss_weight": 256
+            }
+        },
+        {
+            "name": "ribosome",
+            "is_particle": true,
+            "pdb_id": "6EK0",
+            "label": 4,
+            "color": [  0,  92,  49, 255],
+            "radius": 150,
+            "map_threshold": 0.0374,
+            "metadata": {
+                "score_weight": 1,
+                "score_threshold": 0.19,
+                "class_loss_weight": 256
+            }
+        },
+        {
+            "name": "thyroglobulin",
+            "is_particle": true,
+            "pdb_id": "6SCJ",
+            "label": 5,
+            "color": [ 43, 206,  72, 255],
+            "radius": 130,
+            "map_threshold": 0.0278,
+            "metadata": {
+                "score_weight": 2,
+                "score_threshold": 0.18,
+                "class_loss_weight": 256
+            }
+        },
+        {
+            "name": "virus-like-particle",
+            "is_particle": true,
+            "label": 6,
+            "color": [255, 204, 153, 255],
+            "radius": 135,
+            "map_threshold": 0.201,
+            "metadata": {
+                "score_weight": 1,
+                "score_threshold": 0.5,
+                "class_loss_weight": 256
+            }
+        }
+    ],
+    "config_type": "filesystem",
+    "overlay_root": "local:///PATH/TO/EXTRACTED/PROJECT/",
+    "static_root": "local:///PATH/TO/EXTRACTED/PROJECT/"
+}
+```
+
+## Commands
+After installation, use the command `topcup --help` to show all the possible subcomamnds:
+```
+Usage: topcup [OPTIONS] COMMAND [ARGS]...
+
+  topcup: a top crypet u-net picker
+
+Options:
+  -v, --verbose  Increase verbosity (-v, -vv).
+  --version      Show the version and exit.
+  -h, --help     Show this message and exit.
+
+Commands:
+  inference
+  train
+  score
+```
+
+### Training from scratch
+Use `topcup train --help` to see all the options for training. The code support loading data via copick. An example training command is below.
+```
+topcup train \
+    --copick_config COPICK_CONFIG_FILE \
+    --train_run_names TS_6_4,TS_6_6,TS_69_2,TS_73_6,TS_86_3,TS_99_9 \
+    --val_run_names TS_5_4 \
+    --tomo_type denoised \
+    --user_id COPICK_USER_ID \
+    --pixelsize 10 \  
+    --batch_size 16 \
+    --n_aug 1112 \
+    --output_dir OUTPUT_PATH \
+    --logger_version 1 \
+    --epochs 100   
+```
+
+### Re-training from a checkpoint for the same dataset
+```
+topcup train \
+    --copick_config COPICK_CONFIG_FILE \
+    --train_run_names TS_6_4,TS_6_6,TS_69_2,TS_73_6,TS_86_3,TS_99_9 \
+    --val_run_names TS_5_4  \
+    --tomo_type denoised \
+    --user_id COPICK_USER_ID \
+    --pixelsize 10 \  
+    --batch_size 16 \
+    --n_aug 1112 \
+    --output_dir OUTPUT_PATH \
+    --logger_version 1 \
+    --epochs 100 \
+    --pretrained_weight CHECKPOINT_PATH   
+```
+
+### *Subset transfer learning: re-training from a checkpoint for a different dataset 
+**Subset transfer learning** involves loading a checkpoint from a pretrained model and fine-tuning it on a new dataset that includes only a subset of the original classes. To do this correctly, it’s important to know which classes and the corresponding `channel_id` the original model was trained on. This information can be accessed by loading the checkpoint and inspecting the `model.description` attribute. The `copick_config` used for fine-tuning should include the same pickable objects as the original training setup, with updated class weights and thresholds as needed for the new task.
+
+```
+>>> from czii_cryoet_models.model import SegNet
+>>> model = SegNet.load_from_checkpoint('/hpc/projects/group.czii/kevin.zhao/ml_challenge/winning_models/czii_cryoet_mlchallenge_models/output_test/checkpoints/best_model-v6.ckpt')
+>>> print(model.description)
+SegNet model predicting 6 classes
+
+Class details:
+{
+  "apo-ferritin": {
+    "channel_id": 0,
+    "radius": 60.0,
+    "score_threshold": 0.16,
+    "score_weight": 1
+  },
+  "beta-amylase": {
+    "channel_id": 1,
+    "radius": 65.0,
+    "score_threshold": 0.25,
+    "score_weight": 0
+  },
+  "beta-galactosidase": {
+    "channel_id": 2,
+    "radius": 90.0,
+    "score_threshold": 0.13,
+    "score_weight": 2
+  },
+  "ribosome": {
+    "channel_id": 3,
+    "radius": 150.0,
+    "score_threshold": 0.19,
+    "score_weight": 1
+  },
+  "thyroglobulin": {
+    "channel_id": 4,
+    "radius": 130.0,
+    "score_threshold": 0.18,
+    "score_weight": 2
+  },
+  "virus-like-particle": {
+    "channel_id": 5,
+    "radius": 135.0,
+    "score_threshold": 0.5,
+    "score_weight": 1
+  }
+}
+```
+
+
+### Inference
+Use command `topcup inference --help` to see all the options for the inference pipeline. An example command for inference with PyTorch checkpoints (a single checkpoint file path or multiple folder paths, each containing mutiple checkpoints) that supports pattern matching. 
+
+```
+topcup inference \
+    --copick_config copick_config.json \
+    --run_names TS_100_4,TS_100_6,TS_100_7,TS_100_9 \
+    --tomo_type denoised \
+    --user_id COPICK_USER_ID \
+    --pretrained_weights FOLDER_PATH1/checkpoints/,FOLDER_PATH2/checkpoints/,FOLDER_PATH3/checkpoints/ \
+    --batch_size 16 \
+    --output_dir OUTPUT_PATH \
+    --pattern *v1.ckpt 
+```
+
+### Score calculation
+Use command 'topcup score --help' to see all the options for calculating F-beta score for the predictions:
+```
+Usage: topcup score [OPTIONS]
+
+Options:
+  -c, --copick_config FILE  copick config file path  [required]
+  -g, --gt FILE             Ground truth picks csv file path  [required]
+  -s, --submission FILE     Submission picks csv file path  [required]
+  -h, --help                Show this message and exit.
+```
+
+
+## 📚 Documentation
+
+Coming soon.
+
+## 🤝 Contributor covenant code of conduct
+
+This project adheres to the Contributor Covenant code of conduct. By participating, you are expected to uphold this code. Please report unacceptable behavior to opensource@chanzuckerberg.com.
+
+Responsible Use: We are committed to advancing the responsible development and use of artificial intelligence. Please follow our [Acceptable Use Policy](https://virtualcellmodels.cziscience.com/acceptable-use-policy) when engaging with the model.
+
+## 🔒 Security
+
+If you believe you have found a security issue, please responsibly disclose by contacting us at security@chanzuckerberg.com.

topcup-1.0.1/pyproject.toml

@@ -0,0 +1,44 @@
+[build-system]
+requires = ["setuptools>=61.0"]
+build-backend = "setuptools.build_meta"
+
+[project]
+name = "topcup"
+version = "1.0.1"
+description = "An implementation of 2024-2025 Kaggle/CZI cryoET ML challenge winning models"
+authors = [
+    { name="Zhuowen Zhao", email="kevin.zhao@biohub.org" },
+    { name="Christof Henkel", email="chenkel@nvidia.com" },
+    { name="Eugene Khvedchenya", email="ekhvedchenia@nvidia.com" }, 
+]
+readme = "README.md"
+requires-python = ">=3.10"
+dependencies = [
+  "copick",
+  "scikit-learn",
+  "zarr==2.18.2",
+  "numcodecs==0.11.0",
+  "pandas",
+  "einops",
+  "albumentations==1.4.21",
+  "opencv-python==4.12.0.88",
+  "timm==1.0.11",
+  "torch==2.4.*",
+  "torchvision==0.19.*",
+  "pytorch-lightning==2.4.*",
+  "monai==1.5.0",
+  "mrcfile"
+]
+
+[project.urls]
+Homepage = "https://github.com/czimaginginstitute/czii_cryoet_challenge_models"
+
+[project.scripts]
+topcup = "topcup.cli.cli:cli"
+
+[tool.setuptools]
+package-dir = {"" = "src"}
+
+[tool.setuptools.packages.find]
+where = ["src"]
+include = ["topcup*"]

topcup-1.0.1/setup.cfg

@@ -0,0 +1,4 @@
+[egg_info]
+tag_build = 
+tag_date = 0
+

topcup-1.0.1/src/topcup/__init__.py

@@ -0,0 +1,5 @@
+"""
+TopCUP: Top Cryoet U-net Picker
+"""
+
+__version__ = '0.0.6'