leopard-em 0.0.2a0__tar.gz

leopard_em-0.0.2a0/.copier-answers.yml

@@ -0,0 +1,11 @@
+# Do not edit - changes here will be overwritten by Copier
+_commit: v1
+_src_path: gh:pydev-guide/pyrepo-copier
+author_email: jdickerson@berkeley.edu
+author_name: Josh Dickerson
+github_username: jdickerson95
+mode: tooling
+module_name: tt2dtm
+project_name: tt2DTM
+project_short_description: 2DTM in pyTorch
+

leopard_em-0.0.2a0/.github/ISSUE_TEMPLATE.md

@@ -0,0 +1,15 @@
+* Leopard-EM version:
+* Python version:
+* Operating System:
+
+### Description
+
+Describe what you were trying to get done.
+Tell us what happened, what went wrong, and what you expected to happen.
+
+### What I Did
+
+```
+Paste the command(s) you ran and the output.
+If there was a crash, please include the traceback here.
+```

leopard_em-0.0.2a0/.github/TEST_FAIL_TEMPLATE.md

@@ -0,0 +1,12 @@
+---
+title: "{{ env.TITLE }}"
+labels: [bug]
+---
+The {{ workflow }} workflow failed on {{ date | date("YYYY-MM-DD HH:mm") }} UTC
+
+The most recent failing test was on {{ env.PLATFORM }} py{{ env.PYTHON }}
+with commit: {{ sha }}
+
+Full run: https://github.com/{{ repo }}/actions/runs/{{ env.RUN_ID }}
+
+(This post will be updated if another test fails, as long as this issue remains open.)

leopard_em-0.0.2a0/.github/dependabot.yml

@@ -0,0 +1,10 @@
+# https://docs.github.com/github/administering-a-repository/configuration-options-for-dependency-updates
+
+version: 2
+updates:
+  - package-ecosystem: "github-actions"
+    directory: "/"
+    schedule:
+      interval: "weekly"
+    commit-message:
+      prefix: "ci(dependabot):"

leopard_em-0.0.2a0/.github/workflows/ci.yml

@@ -0,0 +1,108 @@
+name: CI
+
+on:
+  push:
+    branches:
+      - main
+    tags:
+      - "v*"
+  pull_request:
+  workflow_dispatch:
+  schedule:
+    # run every week (for --pre release tests)
+    - cron: "0 0 * * 0"
+
+# cancel in-progress runs that use the same workflow and branch
+concurrency:
+  group: ${{ github.workflow }}-${{ github.ref }}
+  cancel-in-progress: true
+
+jobs:
+  check-manifest:
+    # check-manifest is a tool that checks that all files in version control are
+    # included in the sdist (unless explicitly excluded)
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v4
+      - run: pipx run check-manifest
+
+  test:
+    name: ${{ matrix.platform }} (${{ matrix.python-version }})
+    runs-on: ${{ matrix.platform }}
+    strategy:
+      fail-fast: false
+      matrix:
+        python-version: ["3.9", "3.10", "3.11", "3.12""]
+        platform: [ubuntu-latest, macos-latest, windows-latest]
+
+    steps:
+      - uses: actions/checkout@v4
+
+      - name: 🐍 Set up Python ${{ matrix.python-version }}
+        uses: actions/setup-python@v5
+        with:
+          python-version: ${{ matrix.python-version }}
+          cache-dependency-path: "pyproject.toml"
+          cache: "pip"
+
+      - name: Install Dependencies
+        run: |
+          python -m pip install -U pip
+          # if running a cron job, we add the --pre flag to test against pre-releases
+          python -m pip install .[test] ${{ github.event_name == 'schedule' && '--pre' || ''  }}
+
+      - name: 🧪 Run Tests
+        run: pytest --color=yes --cov --cov-report=xml --cov-report=term-missing
+
+      # If something goes wrong with --pre tests, we can open an issue in the repo
+      - name: 📝 Report --pre Failures
+        if: failure() && github.event_name == 'schedule'
+        uses: JasonEtco/create-an-issue@v2
+        env:
+          GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
+          PLATFORM: ${{ matrix.platform }}
+          PYTHON: ${{ matrix.python-version }}
+          RUN_ID: ${{ github.run_id }}
+          TITLE: "[test-bot] pip install --pre is failing"
+        with:
+          filename: .github/TEST_FAIL_TEMPLATE.md
+          update_existing: true
+
+      - name: Coverage
+        uses: codecov/codecov-action@v3
+
+  deploy:
+    name: Deploy
+    needs: test
+    if: success() && startsWith(github.ref, 'refs/tags/') && github.event_name != 'schedule'
+    runs-on: ubuntu-latest
+
+    permissions:
+      # IMPORTANT: this permission is mandatory for trusted publishing on PyPi
+      # see https://docs.pypi.org/trusted-publishers/
+      id-token: write
+      # This permission allows writing releases
+      contents: write
+
+    steps:
+      - uses: actions/checkout@v4
+        with:
+          fetch-depth: 0
+
+      - name: 🐍 Set up Python
+        uses: actions/setup-python@v5
+        with:
+          python-version: "3.x"
+
+      - name: 👷 Build
+        run: |
+          python -m pip install build
+          python -m build
+
+      - name: 🚢 Publish to PyPI
+        uses: pypa/gh-action-pypi-publish@release/v1
+
+      - uses: softprops/action-gh-release@v2
+        with:
+          generate_release_notes: true
+          files: './dist/*'

leopard_em-0.0.2a0/.github/workflows/python-publish.yml

@@ -0,0 +1,108 @@
+name: CI
+
+on:
+  push:
+    branches:
+      - main
+    tags:
+      - "v*"
+  pull_request:
+  workflow_dispatch:
+  schedule:
+    # run every week (for --pre release tests)
+    - cron: "0 0 * * 0"
+
+# cancel in-progress runs that use the same workflow and branch
+concurrency:
+  group: ${{ github.workflow }}-${{ github.ref }}
+  cancel-in-progress: true
+
+jobs:
+  check-manifest:
+    # check-manifest is a tool that checks that all files in version control are
+    # included in the sdist (unless explicitly excluded)
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v4
+      - run: pipx run check-manifest
+
+  test:
+    name: ${{ matrix.platform }} (${{ matrix.python-version }})
+    runs-on: ${{ matrix.platform }}
+    strategy:
+      fail-fast: false
+      matrix:
+        python-version: ["3.10", "3.11", "3.12"]
+        platform: [ubuntu-latest, macos-latest]
+
+    steps:
+      - uses: actions/checkout@v4
+
+      - name: 🐍 Set up Python ${{ matrix.python-version }}
+        uses: actions/setup-python@v5
+        with:
+          python-version: ${{ matrix.python-version }}
+          cache-dependency-path: "pyproject.toml"
+          cache: "pip"
+
+      - name: Install Dependencies
+        run: |
+          python -m pip install -U pip
+          # if running a cron job, we add the --pre flag to test against pre-releases
+          python -m pip install .[test] ${{ github.event_name == 'schedule' && '--pre' || ''  }}
+
+      - name: 🧪 Run Tests
+        run: pytest --color=yes --cov --cov-report=xml --cov-report=term-missing
+
+      # If something goes wrong with --pre tests, we can open an issue in the repo
+      - name: 📝 Report --pre Failures
+        if: failure() && github.event_name == 'schedule'
+        uses: JasonEtco/create-an-issue@v2
+        env:
+          GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
+          PLATFORM: ${{ matrix.platform }}
+          PYTHON: ${{ matrix.python-version }}
+          RUN_ID: ${{ github.run_id }}
+          TITLE: "[test-bot] pip install --pre is failing"
+        with:
+          filename: .github/TEST_FAIL_TEMPLATE.md
+          update_existing: true
+
+      - name: Coverage
+        uses: codecov/codecov-action@v5
+
+  deploy:
+    name: Deploy
+    needs: test
+    if: success() && startsWith(github.ref, 'refs/tags/') && github.event_name != 'schedule'
+    runs-on: ubuntu-latest
+
+    permissions:
+      # IMPORTANT: this permission is mandatory for trusted publishing on PyPi
+      # see https://docs.pypi.org/trusted-publishers/
+      id-token: write
+      # This permission allows writing releases
+      contents: write
+
+    steps:
+      - uses: actions/checkout@v4
+        with:
+          fetch-depth: 0
+
+      - name: 🐍 Set up Python
+        uses: actions/setup-python@v5
+        with:
+          python-version: "3.x"
+
+      - name: 👷 Build
+        run: |
+          python -m pip install build
+          python -m build
+
+      - name: 🚢 Publish to PyPI
+        uses: pypa/gh-action-pypi-publish@release/v1
+
+      - uses: softprops/action-gh-release@v2
+        with:
+          generate_release_notes: true
+          files: './dist/*'

leopard_em-0.0.2a0/.gitignore

@@ -0,0 +1,120 @@
+# Byte-compiled / optimized / DLL files
+__pycache__/
+*.py[cod]
+*$py.class
+
+# C extensions
+*.so
+
+# Distribution / packaging
+.Python
+env/
+build/
+develop-eggs/
+dist/
+downloads/
+eggs/
+.eggs/
+lib/
+lib64/
+parts/
+sdist/
+var/
+wheels/
+*.egg-info/
+.installed.cfg
+*.egg
+
+.DS_Store
+
+# PyInstaller
+#  Usually these files are written by a python script from a template
+#  before PyInstaller builds the exe, so as to inject date/other infos into it.
+*.manifest
+*.spec
+
+# Installer logs
+pip-log.txt
+pip-delete-this-directory.txt
+
+# Unit test / coverage reports
+htmlcov/
+.tox/
+.coverage
+.coverage.*
+.cache
+nosetests.xml
+coverage.xml
+*.cover
+.hypothesis/
+.pytest_cache/
+
+# Translations
+*.mo
+*.pot
+
+# Django stuff:
+*.log
+local_settings.py
+
+# Flask stuff:
+instance/
+.webassets-cache
+
+# Scrapy stuff:
+.scrapy
+
+# Sphinx documentation
+docs/_build/
+
+# PyBuilder
+target/
+
+# Jupyter Notebook
+.ipynb_checkpoints
+
+# pyenv
+.python-version
+
+# celery beat schedule file
+celerybeat-schedule
+
+# SageMath parsed files
+*.sage.py
+
+# dotenv
+.env
+
+# virtualenv
+.venv
+venv/
+ENV/
+
+# Spyder project settings
+.spyderproject
+.spyproject
+
+# Rope project settings
+.ropeproject
+
+# mkdocs documentation
+/site
+
+# mypy
+.mypy_cache/
+
+# ruff
+.ruff_cache/
+
+# IDE settings
+.vscode/
+.idea/
+
+# Temporary files
+*.tmp
+
+
+small_image_test_data/
+medium_image_test_data/
+large_image_test_data/
+scratch_files/

leopard_em-0.0.2a0/.pre-commit-config.yaml

@@ -0,0 +1,39 @@
+# enable pre-commit.ci at https://pre-commit.ci/
+# it adds:
+# 1. auto fixing pull requests
+# 2. auto updating the pre-commit configuration
+ci:
+  autoupdate_schedule: monthly
+  autofix_commit_msg: "style(pre-commit.ci): auto fixes [...]"
+  autoupdate_commit_msg: "ci(pre-commit.ci): autoupdate"
+
+repos:
+  - repo: https://github.com/abravalheri/validate-pyproject
+    rev: v0.22
+    hooks:
+      - id: validate-pyproject
+
+  - repo: https://github.com/crate-ci/typos
+    rev: v1.24.6
+    hooks:
+      - id: typos
+        args:  # omitting --write-changes
+          - "--force-exclude"
+          # - "--config=_typos.toml"
+
+  - repo: https://github.com/astral-sh/ruff-pre-commit
+    rev: v0.7.2
+    hooks:
+      - id: ruff
+        args: [--fix]  # may also add '--unsafe-fixes'
+      - id: ruff-format
+
+  - repo: https://github.com/pre-commit/mirrors-mypy
+    rev: v1.13.0
+    hooks:
+      - id: mypy
+        files: "^src/"
+        # # you have to add the things you want to type check against here
+        # additional_dependencies:
+        #   - numpy
+

leopard_em-0.0.2a0/LICENSE

@@ -0,0 +1,28 @@
+BSD 3-Clause License
+
+Copyright (c) 2024-2025, Josh Dickerson and Matthew Giammar
+
+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.
+
+2. Redistributions in binary form must reproduce the above copyright notice,
+   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.
+
+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.

leopard_em-0.0.2a0/PKG-INFO

@@ -0,0 +1,135 @@
+Metadata-Version: 2.4
+Name: leopard_em
+Version: 0.0.2a0
+Summary: Location & Orientation of Particles using Two-Dimensional Template Matching
+Project-URL: homepage, https://github.com/Lucaslab-Berkeley/Leopard-EM
+Project-URL: repository, https://github.com/Lucaslab-Berkeley/Leopard-EM
+Author-email: Josh Dickerson <jdickerson@berkeley.edu>, Matthew Giammar <matthew_giammar@berkeley.edu>
+License: BSD-3-Clause
+License-File: LICENSE
+Classifier: Development Status :: 3 - Alpha
+Classifier: License :: OSI Approved :: BSD License
+Classifier: Programming Language :: Python :: 3
+Classifier: Programming Language :: Python :: 3.10
+Classifier: Programming Language :: Python :: 3.11
+Classifier: Programming Language :: Python :: 3.12
+Classifier: Typing :: Typed
+Requires-Python: >=3.9
+Requires-Dist: mrcfile
+Requires-Dist: numpy
+Requires-Dist: pandas
+Requires-Dist: pydantic
+Requires-Dist: pyyaml
+Requires-Dist: roma
+Requires-Dist: torch
+Requires-Dist: torch-fourier-filter==v0.2.2
+Requires-Dist: torch-fourier-slice==v0.0.5
+Requires-Dist: torch-image-lerp==v0.0.5
+Requires-Dist: torch-so3>=v0.1.3
+Requires-Dist: tqdm
+Requires-Dist: types-pyyaml
+Provides-Extra: dev
+Requires-Dist: ipython; extra == 'dev'
+Requires-Dist: mypy; extra == 'dev'
+Requires-Dist: pdbpp; extra == 'dev'
+Requires-Dist: pre-commit; extra == 'dev'
+Requires-Dist: rich; extra == 'dev'
+Requires-Dist: ruff; extra == 'dev'
+Provides-Extra: docs
+Requires-Dist: mkdocs; extra == 'docs'
+Requires-Dist: mkdocs-inline-select-svg-plugin; extra == 'docs'
+Requires-Dist: mkdocs-jupyter; extra == 'docs'
+Requires-Dist: mkdocs-material; extra == 'docs'
+Requires-Dist: python-markdown-math; extra == 'docs'
+Provides-Extra: test
+Requires-Dist: pytest; extra == 'test'
+Requires-Dist: pytest-cov; extra == 'test'
+Description-Content-Type: text/markdown
+
+# Leopard-EM: Python based template matching
+
+[![License](https://img.shields.io/pypi/l/Leopard-EM.svg?color=green)](https://github.com/Lucaslab-Berkeley/Leopard-EM/raw/main/LICENSE)
+[![PyPI](https://img.shields.io/pypi/v/Leopard-EM.svg?color=green)](https://pypi.org/project/Leopard-EM)
+[![Python Version](https://img.shields.io/pypi/pyversions/Leopard-EM.svg?color=green)](https://python.org)
+[![CI](https://github.com/Lucaslab-Berkeley/Leopard-EM/actions/workflows/ci.yml/badge.svg)](https://github.com/Lucaslab-Berkeley/Leopard-EM/actions/workflows/ci.yml)
+[![codecov](https://codecov.io/gh/Lucaslab-Berkeley/Leopard-EM/branch/main/graph/badge.svg)](https://github.com/Lucaslab-Berkeley/Leopard-EM)
+
+Leopard-EM (**L**ocation & ori**E**ntati**O**n of **PAR**ticles found using two-**D**imensional t**E**mplate **M**atching) is a python package for running two-dimensional template matching (2DTM) on cryo-EM images.
+
+<!-- ## Documentation and Examples
+
+See the `/examples` directory for a set of Jupyter notebooks demonstrating some basic usage of the package.
+More extensive documentation can be found at (TODO: Add link to documentation site). -->
+
+## Basic Installation
+
+The newest released version of the package can be installed from PyPI using pip:
+
+```bash
+pip install leopard-em
+```
+
+## Usage
+
+### Template Matching
+
+Inputs to the template matching programs can be configured with Pydantic models (see online documentation for examples and use cases).
+Alternatively, configurations can be set in YAML files and loaded into the `MatchTemplateManager` object.
+The [example YAML configuration file](match_template_example_config.yaml) acts as a template for configuring your own runs.
+Once configured with the proper paths, parameters, etc., the program can run as follows:
+
+```python
+from leopard_em.pydantic_models import MatchTemplateManager
+
+YAML_CONFIG_PATH = "path/to/mt_config.yaml"
+ORIENTATION_BATCH_SIZE = 8
+
+def main():
+    mt_manager = MatchTemplateManager.from_yaml(YAML_CONFIG_PATH)
+    mt_manager.run_match_template(ORIENTATION_BATCH_SIZE)
+    df.results_to_dataframe()
+    df.to_csv("/path/to/results.csv")
+
+# NOTE: invoking from `if __name__ == "__main__"` is necessary
+# for proper multiprocessing/GPU-distribution behavior
+if __name__ == "__main__":
+    main()
+```
+
+### Template Refinement
+
+Particle orientations and locations can be refined using the `RefineTemplateManager` objects after a template matching run.
+The `RefineTemplateManager` is similarly a set of Pydantic models capable of configuration via YAML files.
+The [example YAML configuration file](refine_template_example_config.yaml) acts as a template for configuring your own runs.
+Once configured with the proper paths, parameters, etc., the program can run as follows:
+
+```python
+from leopard_em.pydantic_models import RefineTemplateManager
+
+YAML_PATH = "/path/to/rt_config.yaml"
+ORIENTATION_BATCH_SIZE = 80
+
+def main():
+    rt_manager = RefineTemplateManager.from_yaml(YAML_PATH)
+    rt_manager.run_refine_template(
+        output_dataframe_path="/path/to/refined_results.csv",
+        orientation_batch_size=ORIENTATION_BATCH_SIZE,
+    )
+
+
+if __name__ == "__main__":
+    main()
+
+```
+
+## Installation for Development
+
+The package can be installed from source in editable mode with the optional development libraries via pip.
+
+```bash
+git clone https://github.com/Lucaslab-Berkeley/Leopard-EM.git
+cd Leopard-EM
+pip install -e '.[dev,test, docs]'
+```
+
+Further information on development and contributing to the repo can be found in our online documentation.

leopard_em-0.0.2a0/README.md

@@ -0,0 +1,87 @@
+# Leopard-EM: Python based template matching
+
+[![License](https://img.shields.io/pypi/l/Leopard-EM.svg?color=green)](https://github.com/Lucaslab-Berkeley/Leopard-EM/raw/main/LICENSE)
+[![PyPI](https://img.shields.io/pypi/v/Leopard-EM.svg?color=green)](https://pypi.org/project/Leopard-EM)
+[![Python Version](https://img.shields.io/pypi/pyversions/Leopard-EM.svg?color=green)](https://python.org)
+[![CI](https://github.com/Lucaslab-Berkeley/Leopard-EM/actions/workflows/ci.yml/badge.svg)](https://github.com/Lucaslab-Berkeley/Leopard-EM/actions/workflows/ci.yml)
+[![codecov](https://codecov.io/gh/Lucaslab-Berkeley/Leopard-EM/branch/main/graph/badge.svg)](https://github.com/Lucaslab-Berkeley/Leopard-EM)
+
+Leopard-EM (**L**ocation & ori**E**ntati**O**n of **PAR**ticles found using two-**D**imensional t**E**mplate **M**atching) is a python package for running two-dimensional template matching (2DTM) on cryo-EM images.
+
+<!-- ## Documentation and Examples
+
+See the `/examples` directory for a set of Jupyter notebooks demonstrating some basic usage of the package.
+More extensive documentation can be found at (TODO: Add link to documentation site). -->
+
+## Basic Installation
+
+The newest released version of the package can be installed from PyPI using pip:
+
+```bash
+pip install leopard-em
+```
+
+## Usage
+
+### Template Matching
+
+Inputs to the template matching programs can be configured with Pydantic models (see online documentation for examples and use cases).
+Alternatively, configurations can be set in YAML files and loaded into the `MatchTemplateManager` object.
+The [example YAML configuration file](match_template_example_config.yaml) acts as a template for configuring your own runs.
+Once configured with the proper paths, parameters, etc., the program can run as follows:
+
+```python
+from leopard_em.pydantic_models import MatchTemplateManager
+
+YAML_CONFIG_PATH = "path/to/mt_config.yaml"
+ORIENTATION_BATCH_SIZE = 8
+
+def main():
+    mt_manager = MatchTemplateManager.from_yaml(YAML_CONFIG_PATH)
+    mt_manager.run_match_template(ORIENTATION_BATCH_SIZE)
+    df.results_to_dataframe()
+    df.to_csv("/path/to/results.csv")
+
+# NOTE: invoking from `if __name__ == "__main__"` is necessary
+# for proper multiprocessing/GPU-distribution behavior
+if __name__ == "__main__":
+    main()
+```
+
+### Template Refinement
+
+Particle orientations and locations can be refined using the `RefineTemplateManager` objects after a template matching run.
+The `RefineTemplateManager` is similarly a set of Pydantic models capable of configuration via YAML files.
+The [example YAML configuration file](refine_template_example_config.yaml) acts as a template for configuring your own runs.
+Once configured with the proper paths, parameters, etc., the program can run as follows:
+
+```python
+from leopard_em.pydantic_models import RefineTemplateManager
+
+YAML_PATH = "/path/to/rt_config.yaml"
+ORIENTATION_BATCH_SIZE = 80
+
+def main():
+    rt_manager = RefineTemplateManager.from_yaml(YAML_PATH)
+    rt_manager.run_refine_template(
+        output_dataframe_path="/path/to/refined_results.csv",
+        orientation_batch_size=ORIENTATION_BATCH_SIZE,
+    )
+
+
+if __name__ == "__main__":
+    main()
+
+```
+
+## Installation for Development
+
+The package can be installed from source in editable mode with the optional development libraries via pip.
+
+```bash
+git clone https://github.com/Lucaslab-Berkeley/Leopard-EM.git
+cd Leopard-EM
+pip install -e '.[dev,test, docs]'
+```
+
+Further information on development and contributing to the repo can be found in our online documentation.

leopard_em-0.0.2a0/_typos.toml

@@ -0,0 +1,2 @@
+[default.extend-words]
+BA = "BA"