Revise Documentation

.gitignore

@@ -160,4 +160,5 @@ cython_debug/
 #.idea/
 
 
-.DS_store
+# MacOS
+*.DS_store*

docs/Contributing.md → docs/contributing.md

@@ -45,4 +45,4 @@ We welcome any geometric representation of trees in airborne imagery. Points, po
 
 The working document describing technical details of evaluation is still in its infancy is [here](https://docs.google.com/document/d/1K6G1tcdTuAv3FgGiDWq5QhO-kSoBrxzTiic5jH1CZF4/edit?usp=sharing)
 
-## Code
+## Code

docs/Dataset_Structure.md → docs/dataset_structure.md

@@ -1 +1,3 @@
-The organization of this dataset was inspired by the WILDS benchmark
+# Dataset structure
+The organization of this dataset was inspired by the WILDS benchmark
+

docs/Datasets.md → docs/datasets.md

@@ -5,3 +5,4 @@
 ## Boxes
 
 ## Polygons
+

docs/developer.md

@@ -0,0 +1,78 @@
+# Developer's Guide
+
+1. Start by forking the main repository: [https://github.com/weecology/MillionTrees](https://github.com/weecology/MillionTrees).
+2. Clone your fork of the repository:
+
+    - Using HTTPS: `git clone https://github.com/myUserName/MillionTrees.git`
+    - Using SSH: `git clone git@github.com:myUserName/MillionTrees.git`
+
+3. Link your cloned repository to the main repository (typically named `upstream`):
+
+    - `git remote add upstream https://github.com/weecology/MillionTrees.git`
+
+5. Verify your remote settings with:
+
+    ```bash
+    git remote -v
+    ```
+
+    You should see output similar to:
+
+    ```
+    origin    git@github.com:myUserName/MillionTrees.git (fetch)
+    origin    git@github.com:myUserName/MillionTrees.git (push)
+    upstream  https://github.com/weecology/MillionTrees.git (fetch)
+    upstream  https://github.com/weecology/MillionTrees.git (push)
+    ```
+
+6. Install the package from the main directory. Use the `-U` or `--upgrade` flag to update or overwrite any previously installed versions:
+
+    ```bash
+    pip install . -U
+    ```
+
+## Running Tests Locally
+
+[Add specific instructions for running tests if necessary.]
+
+## Create Release
+
+[Add specific instructions for creating a release if necessary.]
+
+## Documentation
+
+We use [Sphinx](http://www.sphinx-doc.org/en/stable/) and [Read the Docs](https://readthedocs.org/) for our documentation. Sphinx supports both reStructuredText and markdown as markup languages. 
+
+Source code documentation is automatically included after committing to the main repository. To add additional supporting documentation, create new reStructuredText or markdown files in the `docs` folder.
+
+If you need to reorganize the documentation, refer to the [Sphinx documentation](http://www.sphinx-doc.org/en/stable/).
+
+### Update Documentation
+
+The documentation is automatically updated for changes within modules. **However, it is essential to update the documentation after adding new modules** in the `engines` or `lib` directories.
+
+1. Navigate to the `docs` directory and create a temporary directory, e.g., `source`.
+2. Run the following command to generate documentation:
+
+    ```bash
+    cd docs
+    mkdir source
+    sphinx-apidoc -f -o ./source /Users/..../MillionTrees/milliontrees/
+    ```
+
+   In this example, `source` is the destination folder for the generated `.rst` files, and `/Users/..../MillionTrees/milliontrees/` is the path to the `milliontrees` source code.
+
+3. Review the generated files, make necessary edits to ensure accuracy, and then commit and push the changes.
+
+### Test Documentation Locally
+
+To test the documentation locally:
+
+    ```bash
+    cd docs  # Navigate to the docs directory
+    make html && python3 -m http.server --directory _build/html
+    ```
+
+   This command generates the HTML files and hosts a local HTTP server on `localhost:8000`, allowing you to view the documentation in your browser.
+
+> **Note:** Do not commit the `_build` directory after generating HTML.

docs/Getting_Started.md → docs/getting_started.md

@@ -1,2 +1,3 @@
 # Getting Started
 
+MillionTrees

docs/index.rst

@@ -27,8 +27,11 @@ Forests underlie many ecosystem services, agricultural systems and urban plannin
    :maxdepth: 2
    :caption: User Guide:
 
-   Getting_Started
-   Datasets
-   Leaderboard
-   Contributing
+   getting_started
+   datasets
+   dataset_structure
+   leaderboard
+   contributing
+   developer
+   source/modules.rst
 

docs/Leaderboard.md → docs/leaderboard.md

@@ -1,5 +1,6 @@
 # Leaderboard
 
+
 | Name | Citation | Official Split | Random Split |
 |------|----------|----------------|--------------|
 |       |            |                  |                |

docs/source/milliontrees.common.metrics.rst

@@ -0,0 +1,37 @@
+milliontrees.common.metrics package
+===================================
+
+Submodules
+----------
+
+milliontrees.common.metrics.all\_metrics module
+-----------------------------------------------
+
+.. automodule:: milliontrees.common.metrics.all_metrics
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+milliontrees.common.metrics.loss module
+---------------------------------------
+
+.. automodule:: milliontrees.common.metrics.loss
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+milliontrees.common.metrics.metric module
+-----------------------------------------
+
+.. automodule:: milliontrees.common.metrics.metric
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+Module contents
+---------------
+
+.. automodule:: milliontrees.common.metrics
+   :members:
+   :undoc-members:
+   :show-inheritance:

docs/source/milliontrees.common.rst

@@ -0,0 +1,45 @@
+milliontrees.common package
+===========================
+
+Subpackages
+-----------
+
+.. toctree::
+   :maxdepth: 4
+
+   milliontrees.common.metrics
+
+Submodules
+----------
+
+milliontrees.common.data\_loaders module
+----------------------------------------
+
+.. automodule:: milliontrees.common.data_loaders
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+milliontrees.common.grouper module
+----------------------------------
+
+.. automodule:: milliontrees.common.grouper
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+milliontrees.common.utils module
+--------------------------------
+
+.. automodule:: milliontrees.common.utils
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+Module contents
+---------------
+
+.. automodule:: milliontrees.common
+   :members:
+   :undoc-members:
+   :show-inheritance:

docs/source/milliontrees.datasets.rst

@@ -0,0 +1,61 @@
+milliontrees.datasets package
+=============================
+
+Subpackages
+-----------
+
+.. toctree::
+   :maxdepth: 4
+
+   milliontrees.datasets.unlabeled
+
+Submodules
+----------
+
+milliontrees.datasets.TreeBoxes module
+--------------------------------------
+
+.. automodule:: milliontrees.datasets.TreeBoxes
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+milliontrees.datasets.TreePoints module
+---------------------------------------
+
+.. automodule:: milliontrees.datasets.TreePoints
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+milliontrees.datasets.TreePolygons module
+-----------------------------------------
+
+.. automodule:: milliontrees.datasets.TreePolygons
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+milliontrees.datasets.download\_utils module
+--------------------------------------------
+
+.. automodule:: milliontrees.datasets.download_utils
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+milliontrees.datasets.milliontrees\_dataset module
+--------------------------------------------------
+
+.. automodule:: milliontrees.datasets.milliontrees_dataset
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+Module contents
+---------------
+
+.. automodule:: milliontrees.datasets
+   :members:
+   :undoc-members:
+   :show-inheritance:

docs/source/milliontrees.datasets.unlabeled.rst

@@ -0,0 +1,37 @@
+milliontrees.datasets.unlabeled package
+=======================================
+
+Submodules
+----------
+
+milliontrees.datasets.unlabeled.TreeBoxesUnlabeled module
+---------------------------------------------------------
+
+.. automodule:: milliontrees.datasets.unlabeled.TreeBoxesUnlabeled
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+milliontrees.datasets.unlabeled.TreePointsUnlabeled module
+----------------------------------------------------------
+
+.. automodule:: milliontrees.datasets.unlabeled.TreePointsUnlabeled
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+milliontrees.datasets.unlabeled.TreePolygonsUnlabeled module
+------------------------------------------------------------
+
+.. automodule:: milliontrees.datasets.unlabeled.TreePolygonsUnlabeled
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+Module contents
+---------------
+
+.. automodule:: milliontrees.datasets.unlabeled
+   :members:
+   :undoc-members:
+   :show-inheritance:

docs/source/milliontrees.rst

@@ -0,0 +1,46 @@
+milliontrees package
+====================
+
+Subpackages
+-----------
+
+.. toctree::
+   :maxdepth: 4
+
+   milliontrees.common
+   milliontrees.datasets
+
+Submodules
+----------
+
+milliontrees.download\_datasets module
+--------------------------------------
+
+.. automodule:: milliontrees.download_datasets
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+milliontrees.get\_dataset module
+--------------------------------
+
+.. automodule:: milliontrees.get_dataset
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+milliontrees.version module
+---------------------------
+
+.. automodule:: milliontrees.version
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+Module contents
+---------------
+
+.. automodule:: milliontrees
+   :members:
+   :undoc-members:
+   :show-inheritance:

docs/source/modules.rst

@@ -0,0 +1,7 @@
+milliontrees
+============
+
+.. toctree::
+   :maxdepth: 4
+
+   milliontrees