Move package into src dir (#828)

weecology · Nov 19, 2024 · fdfd55f · fdfd55f
1 parent def50b9
commit fdfd55f
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Showing 55 changed files with 42 additions and 41 deletions.
diff --git a/.bumpversion.toml b/.bumpversion.toml
@@ -1,5 +1,5 @@
 [tool.bumpversion]
-current_version = "1.4.2-dev0"
+current_version = "1.4.2"
 
 parse = """(?x)
     (?P<major>0|[1-9]\\d*)\\.
@@ -38,4 +38,4 @@ commit_args = ""
 filename = "pyproject.toml"
 
 [[tool.bumpversion.files]]
-filename = "deepforest/_version.py"
+filename = "src/deepforest/_version.py"
diff --git a/.github/workflows/Conda-app.yml b/.github/workflows/Conda-app.yml
@@ -46,11 +46,14 @@ jobs:
           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 deepforest/ --style=.style.yapf
+        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
@@ -59,7 +62,7 @@ jobs:
         run: pytest --nbmake docs/**/*_test.ipynb
 
       - name: Run docformatter
-        run: docformatter --check --recursive deepforest/
+        run: docformatter --check --recursive src/deepforest/
 
       - name: Test Docs
         run: |

diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml
@@ -4,7 +4,7 @@ repos:
   - id: yapf
     name: yapf
     entry: yapf
-    args: ['-i', '--style', '.style.yapf', '--recursive', 'deepforest/']
+    args: ['-i', '--style', '.style.yapf', '--recursive', 'src/deepforest/']
     language: system
     types: [python]
     pass_filenames: false
@@ -16,7 +16,7 @@ repos:
         entry: docformatter
         language: python
         types: [python]
-        args: ['--in-place', '--recursive','deepforest/']
+        args: ['--in-place', '--recursive','src/deepforest/']
         pass_filenames: false
         stages: [commit]
 
diff --git a/CONTRIBUTING.rst b/CONTRIBUTING.rst
@@ -86,7 +86,7 @@ You can also run yapf from the command line to cleanup the style in your changes
 
 .. code-block:: bash
 
-   yapf -i --recursive deepforest/ --style=.style.yapf
+   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.
 
@@ -128,7 +128,7 @@ We use `Docformatter <https://pypi.org/project/docformatter/>`_ for formatting a
 
 .. code-block:: bash
 
-   $ docformatter --in-place --recursive deepforest/
+   $ docformatter --in-place --recursive src/deepforest/
 
 Update Documentation
 ^^^^^^^^^^^^^^^^^^^^

diff --git a/HISTORY.rst b/HISTORY.rst
@@ -2,9 +2,14 @@
 DeepForest Changelog
 ====================
 
-Version 1.4.0 (Date: Oct 9, 2024)
+Version 1.4.1 (Date: Oct 26, 2024)
 ----------------------------------
 
+- **Enhancement:** Use GitHub Actions to publish the package.
+
+Version 1.4.0 (Date: Oct 9, 2024)
+---------------------------------
+
  The major innovations are
 
 1. New model loading framework using HuggingFace. DeepForest models are now available on https://huggingface.co/weecology. The models can be loaded using load_model() and used for inference.

diff --git a/MANIFEST.in b/MANIFEST.in
@@ -1,17 +1,17 @@
-include deepforest/data/deepforest_config.yml
-include deepforest/data/testfile_deepforest.csv
-include deepforest/data/testfile_multi.csv
-include deepforest/data/classes.csv
-include deepforest/data/OSBS_029*
-include deepforest/data/SOAP_031*
-include deepforest/data/SOAP_061*
-include deepforest/data/2019_YELL_2_541000_4977000_image_crop.xml
-include deepforest/data/2019_YELL_2_541000_4977000_image_crop.png
-include deepforest/data/2019_YELL_2_528000_4978000_image_crop2.xml
-include deepforest/data/2019_YELL_2_528000_4978000_image_crop2.png
-include deepforest/data/AWPE*
-include deepforest/data/example.csv
-include deepforest/data/test_tiled.tif
+
+include src/deepforest/data/deepforest_config.yml
+include src/deepforest/data/testfile_deepforest.csv
+include src/deepforest/data/testfile_multi.csv
+include src/deepforest/data/classes.csv
+include src/deepforest/data/OSBS_029*
+include src/deepforest/data/SOAP_031*
+include src/deepforest/data/SOAP_061*
+include src/deepforest/data/2019_YELL_2_541000_4977000_image_crop.xml
+include src/deepforest/data/2019_YELL_2_541000_4977000_image_crop.png
+include src/deepforest/data/2019_YELL_2_528000_4978000_image_crop2.xml
+include src/deepforest/data/2019_YELL_2_528000_4978000_image_crop2.png
+include src/deepforest/data/AWPE*
+include src/deepforest/data/example.csv
 
 include LICENSE
 include dev_requirements.txt

diff --git a/README.md b/README.md
@@ -5,7 +5,7 @@
 [![Version](https://img.shields.io/pypi/v/DeepForest.svg)](https://pypi.python.org/pypi/DeepForest)
 [![PyPI - Downloads](https://img.shields.io/pypi/dm/deepforest)](https://pypi.python.org/pypi/DeepForest)
 [![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.2538143.svg)](https://doi.org/10.5281/zenodo.2538143)
-[![Python Version](https://img.shields.io/badge/python-%3E%3D3.5%2C%20%3C3.13-blue.svg)](https://www.python.org/downloads/)
+[![Python Version](https://img.shields.io/badge/python-%3E%3D3.8%2C%20%3C3.13-blue.svg)](https://www.python.org/downloads/)
 
 ### Conda-forge build status
 

diff --git a/pyproject.toml b/pyproject.toml
@@ -7,7 +7,7 @@ requires = [
 
 [project]
 name = "deepforest"
-version = "1.4.2-dev0"
+version = "1.4.2"
 description = "Tree crown prediction using deep learning retinanets"
 readme = "README.md"
 license = { text = "MIT" }
@@ -73,6 +73,6 @@ dependencies = [
     "tqdm",
     "xmltodict",
 ]
-[tool.setuptools]
-packages = ["deepforest"]
-include-package-data = true
+
+[tool.setuptools.packages.find]
+where = ["src"]
diff --git a/deepforest/IoU.py → src/deepforest/IoU.py b/deepforest/IoU.py → src/deepforest/IoU.py
diff --git a/deepforest/__init__.py → src/deepforest/__init__.py b/deepforest/__init__.py → src/deepforest/__init__.py
diff --git a/deepforest/_version.py → src/deepforest/_version.py b/deepforest/_version.py → src/deepforest/_version.py
@@ -1,2 +1,2 @@
-__version__ = '1.4.2-dev0'
+__version__ = '1.4.2'
 # Version updated using bump-my-version
diff --git a/deepforest/callbacks.py → src/deepforest/callbacks.py b/deepforest/callbacks.py → src/deepforest/callbacks.py
diff --git a/.../2018_SJER_3_252000_4107000_image_477.csv → .../2018_SJER_3_252000_4107000_image_477.csv b/.../2018_SJER_3_252000_4107000_image_477.csv → .../2018_SJER_3_252000_4107000_image_477.csv
diff --git a/.../2018_SJER_3_252000_4107000_image_477.tif → .../2018_SJER_3_252000_4107000_image_477.tif b/.../2018_SJER_3_252000_4107000_image_477.tif → .../2018_SJER_3_252000_4107000_image_477.tif
diff --git a/...SJER_3_252000_4107000_image_477_truth.csv → ...SJER_3_252000_4107000_image_477_truth.csv b/...SJER_3_252000_4107000_image_477_truth.csv → ...SJER_3_252000_4107000_image_477_truth.csv
diff --git a/...019_YELL_2_528000_4978000_image_crop2.png → ...019_YELL_2_528000_4978000_image_crop2.png b/...019_YELL_2_528000_4978000_image_crop2.png → ...019_YELL_2_528000_4978000_image_crop2.png
diff --git a/...019_YELL_2_528000_4978000_image_crop2.xml → ...019_YELL_2_528000_4978000_image_crop2.xml b/...019_YELL_2_528000_4978000_image_crop2.xml → ...019_YELL_2_528000_4978000_image_crop2.xml
diff --git a/...2019_YELL_2_541000_4977000_image_crop.png → ...2019_YELL_2_541000_4977000_image_crop.png b/...2019_YELL_2_541000_4977000_image_crop.png → ...2019_YELL_2_541000_4977000_image_crop.png
diff --git a/...2019_YELL_2_541000_4977000_image_crop.xml → ...2019_YELL_2_541000_4977000_image_crop.xml b/...2019_YELL_2_541000_4977000_image_crop.xml → ...2019_YELL_2_541000_4977000_image_crop.xml
diff --git a/...t/data/AWPE Pigeon Lake 2020 DJI_0005.JPG → ...t/data/AWPE Pigeon Lake 2020 DJI_0005.JPG b/...t/data/AWPE Pigeon Lake 2020 DJI_0005.JPG → ...t/data/AWPE Pigeon Lake 2020 DJI_0005.JPG
diff --git a/deepforest/data/OSBS_029.csv → src/deepforest/data/OSBS_029.csv b/deepforest/data/OSBS_029.csv → src/deepforest/data/OSBS_029.csv
diff --git a/deepforest/data/OSBS_029.png → src/deepforest/data/OSBS_029.png b/deepforest/data/OSBS_029.png → src/deepforest/data/OSBS_029.png
diff --git a/deepforest/data/OSBS_029.tif → src/deepforest/data/OSBS_029.tif b/deepforest/data/OSBS_029.tif → src/deepforest/data/OSBS_029.tif
diff --git a/deepforest/data/OSBS_029.xml → src/deepforest/data/OSBS_029.xml b/deepforest/data/OSBS_029.xml → src/deepforest/data/OSBS_029.xml
diff --git a/deepforest/data/SOAP_031.png → src/deepforest/data/SOAP_031.png b/deepforest/data/SOAP_031.png → src/deepforest/data/SOAP_031.png
diff --git a/deepforest/data/SOAP_061.png → src/deepforest/data/SOAP_061.png b/deepforest/data/SOAP_061.png → src/deepforest/data/SOAP_061.png
diff --git a/deepforest/data/SOAP_061.xml → src/deepforest/data/SOAP_061.xml b/deepforest/data/SOAP_061.xml → src/deepforest/data/SOAP_061.xml
diff --git a/deepforest/data/__init__.py → src/deepforest/data/__init__.py b/deepforest/data/__init__.py → src/deepforest/data/__init__.py
diff --git a/deepforest/data/australia.cpg → src/deepforest/data/australia.cpg b/deepforest/data/australia.cpg → src/deepforest/data/australia.cpg
diff --git a/deepforest/data/australia.dbf → src/deepforest/data/australia.dbf b/deepforest/data/australia.dbf → src/deepforest/data/australia.dbf
diff --git a/deepforest/data/australia.prj → src/deepforest/data/australia.prj b/deepforest/data/australia.prj → src/deepforest/data/australia.prj
diff --git a/deepforest/data/australia.shp → src/deepforest/data/australia.shp b/deepforest/data/australia.shp → src/deepforest/data/australia.shp
diff --git a/deepforest/data/australia.shx → src/deepforest/data/australia.shx b/deepforest/data/australia.shx → src/deepforest/data/australia.shx
diff --git a/deepforest/data/australia.tif → src/deepforest/data/australia.tif b/deepforest/data/australia.tif → src/deepforest/data/australia.tif
diff --git a/deepforest/data/classes.csv → src/deepforest/data/classes.csv b/deepforest/data/classes.csv → src/deepforest/data/classes.csv
diff --git a/deepforest/data/deepforest_config.yml → src/deepforest/data/deepforest_config.yml b/deepforest/data/deepforest_config.yml → src/deepforest/data/deepforest_config.yml
diff --git a/deepforest/data/example.csv → src/deepforest/data/example.csv b/deepforest/data/example.csv → src/deepforest/data/example.csv
diff --git a/deepforest/data/test_tiled.tif → src/deepforest/data/test_tiled.tif b/deepforest/data/test_tiled.tif → src/deepforest/data/test_tiled.tif
diff --git a/deepforest/data/testfile_deepforest.csv → src/deepforest/data/testfile_deepforest.csv b/deepforest/data/testfile_deepforest.csv → src/deepforest/data/testfile_deepforest.csv
diff --git a/deepforest/data/testfile_multi.csv → src/deepforest/data/testfile_multi.csv b/deepforest/data/testfile_multi.csv → src/deepforest/data/testfile_multi.csv
diff --git a/deepforest/dataset.py → src/deepforest/dataset.py b/deepforest/dataset.py → src/deepforest/dataset.py
diff --git a/deepforest/download.py → src/deepforest/download.py b/deepforest/download.py → src/deepforest/download.py
diff --git a/deepforest/evaluate.py → src/deepforest/evaluate.py b/deepforest/evaluate.py → src/deepforest/evaluate.py
diff --git a/deepforest/main.py → src/deepforest/main.py b/deepforest/main.py → src/deepforest/main.py
diff --git a/deepforest/model.py → src/deepforest/model.py b/deepforest/model.py → src/deepforest/model.py
diff --git a/deepforest/models/FasterRCNN.py → src/deepforest/models/FasterRCNN.py b/deepforest/models/FasterRCNN.py → src/deepforest/models/FasterRCNN.py
diff --git a/deepforest/models/__init__.py → src/deepforest/models/__init__.py b/deepforest/models/__init__.py → src/deepforest/models/__init__.py
diff --git a/deepforest/models/retinanet.py → src/deepforest/models/retinanet.py b/deepforest/models/retinanet.py → src/deepforest/models/retinanet.py
diff --git a/deepforest/predict.py → src/deepforest/predict.py b/deepforest/predict.py → src/deepforest/predict.py
@@ -1,5 +1,4 @@
 # Prediction utilities
-import cv2
 import pandas as pd
 import numpy as np
 import os

diff --git a/deepforest/preprocess.py → src/deepforest/preprocess.py b/deepforest/preprocess.py → src/deepforest/preprocess.py
@@ -13,8 +13,6 @@
 import warnings
 import rasterio
 import geopandas as gpd
-from shapely import geometry
-import geopandas as gpd
 from deepforest.utilities import read_file, determine_geometry_type
 from shapely import geometry
 

diff --git a/deepforest/utilities.py → src/deepforest/utilities.py b/deepforest/utilities.py → src/deepforest/utilities.py
diff --git a/deepforest/visualize.py → src/deepforest/visualize.py b/deepforest/visualize.py → src/deepforest/visualize.py
diff --git a/tests/conftest.py b/tests/conftest.py
@@ -1,7 +1,8 @@
 # Fixtures model to only download model once
 # download latest release
 import pytest
-from deepforest import utilities, main
+from deepforest import main
+from deepforest import utilities
 from deepforest import get_data
 from deepforest import _ROOT
 import os
@@ -12,8 +13,7 @@
 
 @pytest.fixture(scope="session")
 def config():
-    config = utilities.read_config("{}/deepforest_config.yml".format(
-        os.path.dirname(_ROOT)))
+    config = utilities.read_config(get_data("deepforest_config.yml"))
     config["fast_dev_run"] = True
     config["batch_size"] = True
     return config

diff --git a/tests/test_data.py b/tests/test_data.py
@@ -16,8 +16,3 @@ def test_get_data():
     assert os.path.exists(deepforest.get_data("classes.csv"))
 
 
-# Assert that the included config file matches the front of the repo.
-def test_matching_config(ROOT):
-    config = read_config("{}/deepforest_config.yml".format(os.path.dirname(ROOT)))
-    config_from_data_dir = read_config("{}/data/deepforest_config.yml".format(ROOT))
-    assert config == config_from_data_dir
diff --git a/tests/test_utilities.py b/tests/test_utilities.py
@@ -10,7 +10,8 @@
 import geopandas as gpd
 
 from deepforest import get_data
-from deepforest import utilities, visualize
+from deepforest import visualize
+from deepforest import utilities
 from deepforest import main
 
 # import general model fixture