deepforest 1.4.0.dev0__tar.gz → 1.5.1.dev0__tar.gz

deepforest-1.5.1.dev0/.bumpversion.toml

@@ -0,0 +1,41 @@
+[tool.bumpversion]
+current_version = "1.5.1-dev0"
+
+parse = """(?x)
+    (?P<major>0|[1-9]\\d*)\\.
+    (?P<minor>0|[1-9]\\d*)\\.
+    (?P<patch>0|[1-9]\\d*)
+    (?:
+        -                             # dash separator for pre-release section
+        (?P<pre_l>[a-zA-Z-]+)         # pre-release label
+        (?P<pre_n>0|[1-9]\\d*)        # pre-release version number
+    )?                                # pre-release section is optional
+"""
+serialize = [
+    "{major}.{minor}.{patch}",
+    "{major}.{minor}.{patch}-{pre_l}{pre_n}"
+]
+
+[tool.bumpversion.parts.pre_l]
+values = ["dev", "rc", "final"]
+optional_value = "final"
+
+search = "{current_version}"
+replace = "{new_version}"
+regex = false
+ignore_missing_version = false
+ignore_missing_files = false
+tag = true
+sign_tags = false
+tag_name = "v{new_version}"
+tag_message = "Bump version: {current_version} → {new_version}"
+allow_dirty = false
+commit = true                # Commit after bumping the version
+message = "Bump version: {current_version} → {new_version}"
+commit_args = ""
+
+[[tool.bumpversion.files]]
+filename = "pyproject.toml"
+
+[[tool.bumpversion.files]]
+filename = "src/deepforest/_version.py"

deepforest-1.5.1.dev0/.github/ISSUE_TEMPLATE/bug_report.md

@@ -0,0 +1,45 @@
+---
+name: Bug report
+about: Create a report to help us improve
+title: ''
+labels: ''
+assignees: ''
+
+---
+
+**Describe the bug**
+A clear and concise description of what the bug is. For questions and community discussion, please create a discussion (https://github.com/weecology/DeepForest/discussions). 
+
+**To Reproduce**
+If possible provide a simple code example, using data from the package itself, that reproduces the behavior. The code block below is a starting point. Issues without reproducible code that we can use to explore the problem are much more difficult to understand and debug and so are much less likely to be addressed quickly. Spending some time creating a reproducible example makes it easier for us to help.
+
+```
+# Load the modules
+from deepforest import main
+from deepforest import get_data
+import os
+
+# Use the latest release
+m = main.deepforest()
+m.use_release()
+
+# Use package data for simple training example
+m.config["train"]["csv_file"] = get_data("example.csv") 
+m.config["train"]["root_dir"] = os.path.dirname(get_data("example.csv"))
+m.config["train"]["fast_dev_run"] = True    
+m.trainer.fit(m)
+```
+
+**Environment (please complete the following information):**
+ - OS: 
+ - Python version and environment : 
+
+**Screenshots and Context**
+If applicable, add screenshots to help explain your problem. Please paste entire code instead of a snippet! 
+
+**User Story**
+Tell us about who you are and what you hope to achieve with DeepForest
+
+“As a [type of user] I want [my goal] so that [my reason].”
+
+

deepforest-1.5.1.dev0/.github/ISSUE_TEMPLATE/data_contribution.md

@@ -0,0 +1,26 @@
+---
+name: Data Contribution
+about: Contribute RGB data and annotations for training open-source release models
+title: 'Data Contribution: '
+labels: 'data'
+assignees: 'bw4sz'
+
+---
+
+**Data Description:**
+Provide details on the data, like its location, the number of annotations, format, and the date of collection.
+
+**Data Availability:**
+Specify if the data is available online and mention any recommended platforms for data archiving, such as Zenodo. Additionally, express openness to various data sources and formats.
+
+**RGB Imagery Collection:**
+Explain how the RGB data imagery was collected and state the image resolution.
+
+**Usage Restrictions:**
+Outline any restrictions associated with using this data in the development of a release model.
+
+**Licensing Information:**
+If the data is associated with a license, provide details then name.
+
+**Contact Information:**
+Include relevant contact information for further inquiries or clarification.

deepforest-1.5.1.dev0/.github/ISSUE_TEMPLATE/feature_request.md

@@ -0,0 +1,20 @@
+---
+name: Feature request
+about: Suggest an idea for this project
+title: ''
+labels: ''
+assignees: ''
+
+---
+
+**Please describe A feature you would like to be added.**
+A clear and concise description of what the problem is. Ex. I'm always frustrated when [...]
+
+**Describe the solution you'd like**
+A clear and concise description of what you want to happen.
+
+**Describe alternatives you've considered**
+A clear and concise description of any alternative solutions or features you've considered.
+
+**Additional context**
+Add any other context or screenshots about the feature request here.

deepforest-1.5.1.dev0/.github/workflows/Conda-app.yml

@@ -0,0 +1,73 @@
+name: Conda package
+
+on:
+  push:
+    branches: [ main ]
+  pull_request:
+    branches: [ main ]
+
+jobs:
+  ci:
+    name: "CI setup"
+
+    strategy:
+      fail-fast: false
+      matrix:
+        python-version:
+          - "3.12"
+          - "3.11"
+          - "3.10"
+
+        os:
+          - "ubuntu-latest"
+
+    runs-on: "${{ matrix.os }}"
+
+    # use bash everywhere
+    defaults:
+      run:
+        shell: "bash -l {0}"
+
+    steps:
+      - name: "Checkout code"
+        uses: "actions/checkout@v4"
+
+      - name: Install opencv dependencies
+        run: |
+          sudo apt-get update
+          sudo apt-get install -y libgl1 and libglx-mesa0 
+
+      - name: Install Conda environment with Micromamba
+        uses: mamba-org/setup-micromamba@v1
+        with:
+          environment-name: DeepForest
+          environment-file: environment.yml
+          create-args: "python=${{ matrix.python-version }}"
+          cache-environment: true
+          cache-downloads: true
+
+      - name: Install package
+        run: pip install . -U
+
+      - name: Run pytest
+        run: pytest -v
+
+      - name: Check style
+        run: yapf -d --recursive src/deepforest/ --style=.style.yapf
+
+      - name: Check notebook style
+        run: nbqa yapf --in-place docs/user_guide/examples/*.ipynb --style=.style.yapf
+
+      - name: Check notebook build
+        run: pytest --nbmake docs/**/*_test.ipynb
+
+      - name: Run docformatter
+        run: docformatter --check --recursive src/deepforest/
+
+      - name: Test Docs
+        run: |
+          cd docs && make clean && make html SPHINXOPTS="-W"
+
+      - name: Test and check build artifacts
+        run: |
+          pip install build && python -m build && twine check dist/*

deepforest-1.5.1.dev0/.github/workflows/automate-waiting-labels.yml

@@ -0,0 +1,35 @@
+name: Remove waiting labels after new comment
+on:
+  issue_comment:
+    types: [created]
+  pull_request_review_comment:
+    types: [created]
+
+permissions:
+  issues: write # allow removing label from issue
+  pull-requests: write # allow removing label from PR
+
+jobs:
+  remove-label:
+    runs-on: ubuntu-latest
+    steps:
+    - name: Remove label
+      uses: actions/github-script@v5
+      with:
+        script: |
+          const issueNumber = context.issue.number || context.pull_request.number;
+          const repo = context.repo;
+          const labelToRemove = "Awaiting author contribution";
+
+          const { data: issueLabels } = await github.rest.issues.listLabelsOnIssue({
+            ...repo,
+            issue_number: issueNumber
+          });
+
+          if (issueLabels.find(label => label.name === labelToRemove)) {
+            await github.rest.issues.removeLabel({
+              ...repo,
+              issue_number: issueNumber,
+              name: labelToRemove
+            });
+          }

deepforest-1.5.1.dev0/.github/workflows/publish.yml

@@ -0,0 +1,49 @@
+name: Publish to PyPI and Test PyPI
+
+on:
+  push:
+    tags:
+      - '*'
+
+jobs:
+  publish:
+    runs-on: ubuntu-latest
+
+    strategy:
+      matrix:
+        index-url: ['https://test.pypi.org/legacy/', 'https://upload.pypi.org/legacy/']
+
+    steps:
+      - name: Check out repository
+        uses: actions/checkout@v3
+        with:
+          fetch-depth: 0  # Ensure the full repository is checked out
+
+      - name: Set up Python
+        uses: actions/setup-python@v4
+        with:
+          python-version: 3.9
+
+      - name: Install dependencies
+        run: |
+          python -m pip install --upgrade pip build twine
+
+      - name: Build the package
+        run: |
+          python -m build  # Automatically detects `pyproject.toml`
+
+      - name: Publish to Test PyPI or PyPI
+        env:
+          TWINE_USERNAME: __token__
+          TWINE_PASSWORD: ${{ secrets.TEST_PYPI_TOKEN }}
+        run: |
+          if [[ "${{ matrix.index-url }}" == "https://upload.pypi.org/legacy/" ]]; then
+            export TWINE_PASSWORD=${{ secrets.PYPI_TOKEN }}
+          else
+            export TWINE_PASSWORD=${{ secrets.TEST_PYPI_TOKEN }}
+          fi
+          if [[ "${{ matrix.index-url }}" == "https://upload.pypi.org/legacy/" && "${GITHUB_REF_NAME}" == *-dev* ]]; then
+            echo "Skipping publish to PyPI for dev version."
+            exit 0
+          fi
+          twine upload --repository-url ${{ matrix.index-url }} dist/*

deepforest-1.5.1.dev0/.gitignore

@@ -0,0 +1,23 @@
+.coverage
+.DS_Store
+.idea
+.RHistory
+*__pycache__*
+*.egg-info
+*.h5
+*.pl
+*.prof
+*.pt
+*.wp*
+build/
+current_bird_release.csv
+current_release.csv
+docs/_build/
+env/
+lightning_logs/*
+public/
+tests/__pycache__
+tests/data/*
+.vscode/
+*ipynb_checkpoints/
+docs/user_guide/deepforestr.md

deepforest-1.5.1.dev0/.pre-commit-config.yaml

@@ -0,0 +1,22 @@
+repos:
+- repo: local
+  hooks:
+  - id: yapf
+    name: yapf
+    entry: yapf
+    args: ['-i', '--style', '.style.yapf', '--recursive', 'src/deepforest/']
+    language: system
+    types: [python]
+    pass_filenames: false
+    stages: [pre-commit]
+-   repo: local
+    hooks:
+    -   id: docformatter
+        name: docformatter
+        entry: docformatter
+        language: python
+        types: [python]
+        args: ['--in-place', '--recursive','src/deepforest/']
+        pass_filenames: false
+        stages: [pre-commit]
+

deepforest-1.5.1.dev0/.readthedocs.yml

@@ -0,0 +1,19 @@
+version: 2
+
+build:
+  os: ubuntu-22.04
+  tools:
+    python: "3.12"
+
+python:
+  install:
+    - requirements: dev_requirements.txt
+    - method: pip
+      path: .
+
+submodules:
+  include: []
+
+sphinx:
+  # Path to your Sphinx configuration file.
+  configuration: docs/conf.py

deepforest-1.5.1.dev0/.style.yapf

@@ -0,0 +1,4 @@
+[style]
+# YAPF uses the chromium style
+based_on_style = google
+COLUMN_LIMIT=90

deepforest-1.5.1.dev0/.zenodo.json

@@ -0,0 +1,51 @@
+{
+    "creators": [
+      {
+        "affiliation": "University of Florida",
+        "name": "Ethan P. White",
+        "orcid": "0000-0001-6728-7745"
+      },
+      {
+        "affiliation": "University of Florida",
+        "name": "Ben G. Weinstein",
+        "orcid": "0000-0002-2176-7935"
+      },
+      {
+        "affiliation": "University of Florida",
+        "name": "Henry Senyondo",
+        "orcid": "0000-0001-7105-5808"
+      },
+      {
+        "affiliation": "University of Florida",
+        "name": "Muhammed Magdy",
+        "orcid": "0009-0009-6167-7246"
+      },
+      {
+        "affiliation": "University of Mumbai",
+        "name": "Om Doiphode",
+        "orcid": "0009-0007-2592-7370"
+      },
+      {
+        "affiliation": "Columbia University",
+        "name": "Dingyi Fang",
+        "orcid": "0009-0006-8532-5024"
+      }
+    ],
+    "keywords": [
+      "AI",
+      "ML",
+      "remote sensing",
+      "drone",
+      "birds",
+      "Deep Learning",
+      "Object Detection",
+      "Geospatial",
+      "Tree Detection",
+      "Environmental Monitoring",
+      "Remote Sensing",
+      "Annotation Handling",
+      "Multi-Domain Detection"
+    ],
+    "license": "MIT",
+    "upload_type": "software"
+  }

{deepforest-1.4.0.dev0 → deepforest-1.5.1.dev0}/AUTHORS.rst

@@ -18,16 +18,20 @@ Primary Authors
 
     @ethanwhite is a PI and Author of DeepForest.
 
-Other Contributors
-==================
+* `Om Doiphode <https://github.com/Om-Doiphode>`_
 
-The incomplete list of individuals below have provided patches or otherwise
-contributed to the project.
-Check GitHub for recent `contributors <https://github.com/weecology/DeepForest/graphs/contributors>`_.
-We would like to thank everyone who has contributed to the project in any way.
+    @Om-Doiphode is an Author.
 
-* `Henry Senyondo <https://github.com/henrykironde>`_
+* `Muhammed Magdy <https://github.com/Mu-Magdy>`_
+
+    @Mu-Magdy is an Author.
 
 * `Dingyi Fang <https://github.com/dingyif>`_
 
-* `Shawn Taylor <https://github.com/sdtaylor>`_
+    @dingyif is an Author.
+
+Other Contributors
+==================
+
+Check GitHub for recent `contributors <https://github.com/weecology/DeepForest/graphs/contributors>`_.
+We would like to thank everyone who has contributed to the project in any way.

deepforest-1.5.1.dev0/CITATION.cff

@@ -0,0 +1,43 @@
+cff-version: 1.2.0
+message: "If you use this software, please cite it as below. You should also cite the model being used. See the README.md for more information."
+title: "DeepForest: A Python package for RGB deep learning tree crown delineation"
+doi: "10.1111/2041-210X.13472"
+date-released: 2020-08-28
+
+authors:
+  - family-names: "Weinstein"
+    given-names: "Ben G."
+  - family-names: "Marconi"
+    given-names: "Sergio"
+  - family-names: "Aubry-Kientz"
+    given-names: "Mélaine"
+  - family-names: "Vincent"
+    given-names: "Gregoire"
+  - family-names: "Senyondo"
+    given-names: "Henry"
+  - family-names: "White"
+    given-names: "Ethan P."
+
+preferred-citation:
+  title: "DeepForest: A Python package for RGB deep learning tree crown delineation"
+  doi: "10.1111/2041-210X.13472"
+  year: 2020
+  authors:
+    - family-names: "Weinstein"
+      given-names: "Ben G."
+    - family-names: "Marconi"
+      given-names: "Sergio"
+    - family-names: "Aubry-Kientz"
+      given-names: "Mélaine"
+    - family-names: "Vincent"
+      given-names: "Gregoire"
+    - family-names: "Senyondo"
+      given-names: "Henry"
+    - family-names: "White"
+      given-names: "Ethan P."
+  type: article
+  journal: "Methods in Ecology and Evolution"
+  volume: 11
+  issue: 12
+  pages: 1743-1751
+  

deepforest-1.5.1.dev0/CONTRIBUTING.rst

@@ -0,0 +1,184 @@
+Developer's Guide
+=================
+
+Depends on Python 3.5+
+
+Getting started
+---------------
+
+1. Quickstart by forking the `main repository <https://github.com/weecology/DeepForest>`_
+
+2. Clone your copy of the repository.
+
+   - **Using ssh**:
+   
+     ``git clone git@github.com:[your user name]/DeepForest.git``
+
+   - **Using https**:
+
+     ``git clone https://github.com/[your user name]/DeepForest.git``
+
+3. Link or point your cloned copy to the main repository. (I always
+   name it upstream)
+
+   ``git remote add upstream https://github.com/weecology/DeepForest.git``
+
+4. Check or confirm your settings using ``git remote -v``
+
+   .. code-block:: text
+
+      origin git@github.com:[your user name]/DeepForest.git (fetch)
+      origin git@github.com:[your user name]/DeepForest.git (push)
+      upstream https://github.com/weecology/DeepForest.git (fetch)
+      upstream https://github.com/weecology/DeepForest.git (push)
+
+5. Install the package from the main directory.
+
+Deepforest can be installed using either pip or conda.
+
+**Install using Pip**
+
+Installing with Pip uses `dev_requirements.txt <https://github.com/weecology/DeepForest/blob/main/dev_requirements.txt>`_.
+
+.. code-block:: bash
+
+   $ pip install -r dev_requirements.txt
+   $ pip install . -U
+
+**Install using Conda**
+
+Installing with Conda uses `environment.yaml <https://github.com/weecology/DeepForest/blob/main/environment.yml>`_.
+
+Conda-based installs can be slow. We recommend using
+`mamba <https://mamba.readthedocs.io/en/latest/user_guide/mamba.html#quickstart>`_ to speed them up.
+
+.. code-block:: bash
+
+   $ conda create -n deepforest python=3
+   $ conda activate deepforest
+   $ pip install . -U
+
+7. Check if the package was installed; please test using the `sample code <https://deepforest.readthedocs.io/en/latest/getting_started.html>`_.
+
+Testing
+-------
+
+Running tests locally
+^^^^^^^^^^^^^^^^^^^^^
+
+.. code-block:: bash
+
+   $ pip install . --upgrade  # or python setup.py install
+   $ pytest -v
+
+Checking and fixing code style
+^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
+
+Using Yapf
+""""""""""
+
+We use `yapf <https://github.com/google/yapf>`_ for code formatting and style checking.
+
+The easiest way to make sure your code is formatted correctly is to integrate it into your editor.
+See `EDITOR SUPPORT <https://github.com/google/yapf/blob/main/EDITOR%20SUPPORT.md>`_.
+
+You can also run yapf from the command line to cleanup the style in your changes:
+
+.. code-block:: bash
+
+   yapf -i --recursive src/deepforest/ --style=.style.yapf
+
+If the style tests fail on a pull request, running the above command is the easiest way to fix this.
+
+Using pre-commit
+""""""""""""""""
+
+We configure all our checks using the `.pre-commit-config.yaml` file. To verify your code styling before committing, you should run ``pre-commit install`` to set up the hooks, followed by ``pre-commit run`` to execute them. This will apply the formatting rules specified in the .style.yapf file. For additional information, please refer to the `pre-commit documentation <https://pre-commit.com/index.html>`_.
+
+Testing the Conda Deepforest Build
+^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
+
+We use the `conda_recipe/meta.yaml` to make sure that the conda build can build the package.
+
+.. code-block:: bash
+
+   $ cd conda_recipe
+   $ conda build conda_recipe/meta.yaml -c conda-forge -c defaults
+
+Conda staged recipe update
+^^^^^^^^^^^^^^^^^^^^^^^^^^
+
+Update the Conda recipe after every release.
+
+Clone the `Weecology staged recipes <https://github.com/weecology/staged-recipes>`_.
+Checkout the deepforest branch, update the `deepforest/meta.yaml` with the new version and the sha256 values. Sha256 values are obtained from the source on `PYPI download files <https://pypi.org/project/deepforest/#files>`_ using the deepforest-{version-number}.tar.gz.
+
+.. code-block:: jinja
+
+   {% set version = "fill new" %}
+   {% set sha256 = "fill new" %}
+
+
+Documentation
+-------------
+
+We are using `Sphinx <http://www.sphinx-doc.org/en/stable/>`_ and `Read the Docs <https://readthedocs.org/>`_ for the documentation.
+
+We use `Docformatter <https://pypi.org/project/docformatter/>`_ for formatting and style checking.
+
+.. code-block:: bash
+
+   $ docformatter --in-place --recursive src/deepforest/
+
+Update Documentation
+^^^^^^^^^^^^^^^^^^^^
+
+The documentation is automatically updated for changes in functions.
+However, the documentation should be updated after the addition of new functions or modules.
+
+Change to the docs directory and use ``sphinx-apidoc`` to update the doc's `source`. Exclude the tests and setup.py documentation.
+
+Run
+
+.. code-block:: bash
+
+   sphinx-apidoc -f -o ./source ../ ../tests/* ../setup.py
+
+The `source` is the destination folder for the source rst files. `../`
+is the path to where the deepforest source code is located relative to
+the doc directory.
+
+Test documentation locally
+^^^^^^^^^^^^^^^^^^^^^^^^^^
+
+.. code-block:: bash
+
+   cd docs  # Go to the docs directory and install the current changes.
+   pip install ../ -U
+   make clean  # Run
+   make html  # Run
+
+Create Release
+--------------
+
+Start
+^^^^^
+
+1. **Run Pytest tests** – seriously, run them now. And Test build artifacts
+   - Run `Pytest -v`
+   - Run pip install build && python -m build && twine check dist/*
+2. Ensure `HISTORY.rst` is up to date with all changes since the last release.
+3. Use `bump-my-version show-bump` to determine the appropriate version bump.
+4. Update the version for release: `bump-my-version bump [minor | patch | pre_l | pre_n]`. If show-bump does not have the right option, we can manually set it `bump-my-version bump --new-version 1.4.0`
+5. Publish the release to PyPi and update the Conda package.
+    - All releases are done on GitHub Actions when a new tag is push
+    - `git tag v1.0.0`
+    - `git push origin v1.0.0`
+6. Post-release, update the version to the next development iteration:
+   - Run `bump-my-version show-bump` to check the target version.
+   - Then, execute `bump-my-version bump [minor | patch | pre_l | pre_n]`.
+
+Note:
+Do not commit the build directory after making html.
+
+This version correctly follows reStructuredText (reST) conventions and includes code blocks, inline literals, and proper linking. Let me know if you need further adjustments!