update: installation manual and project strutcture

NINAnor · Feb 28, 2024 · dc34e63 · dc34e63
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diff --git a/docs/doctrees/environment.pickle b/docs/doctrees/environment.pickle
diff --git a/docs/doctrees/methods/01_tree_detection/README.doctree b/docs/doctrees/methods/01_tree_detection/README.doctree
diff --git a/docs/doctrees/methods/01_tree_detection/installation_manual.doctree b/docs/doctrees/methods/01_tree_detection/installation_manual.doctree
diff --git a/docs/doctrees/methods/01_tree_detection/project_structure.doctree b/docs/doctrees/methods/01_tree_detection/project_structure.doctree
diff --git a/docs/doctrees/methods/02_support_tools/README.doctree b/docs/doctrees/methods/02_support_tools/README.doctree
diff --git a/docs/doctrees/methods/02_support_tools/README_integration.doctree b/docs/doctrees/methods/02_support_tools/README_integration.doctree
diff --git a/docs/doctrees/methods/02_support_tools/installation_manual.doctree b/docs/doctrees/methods/02_support_tools/installation_manual.doctree
diff --git a/docs/doctrees/methods/02_support_tools/project_structure.doctree b/docs/doctrees/methods/02_support_tools/project_structure.doctree
diff --git a/docs/doctrees/methods/04_urban_climate/README.doctree b/docs/doctrees/methods/04_urban_climate/README.doctree
diff --git a/docs/doctrees/methods/05_tree_visibility/README.doctree b/docs/doctrees/methods/05_tree_visibility/README.doctree
diff --git a/docs/doctrees/methods/05_tree_visibility/installation_manual.doctree b/docs/doctrees/methods/05_tree_visibility/installation_manual.doctree
diff --git a/docs/doctrees/methods/05_tree_visibility/params.doctree b/docs/doctrees/methods/05_tree_visibility/params.doctree
diff --git a/docs/doctrees/methods/05_tree_visibility/tables.doctree b/docs/doctrees/methods/05_tree_visibility/tables.doctree
diff --git a/docs/doctrees/methods/index.doctree b/docs/doctrees/methods/index.doctree
diff --git a/docs/doctrees/methods/installation_manuals/index.doctree b/docs/doctrees/methods/installation_manuals/index.doctree
diff --git a/docs/doctrees/methods/method_template.doctree b/docs/doctrees/methods/method_template.doctree
diff --git a/docs/html/_images/workflow.png b/docs/html/_images/workflow.png
diff --git a/...ource/methods/01_tree_detection/index.rst → .../methods/01_tree_detection/README.rst.txt b/...ource/methods/01_tree_detection/index.rst → .../methods/01_tree_detection/README.rst.txt
@@ -2,8 +2,6 @@
 Task 1 | Urban Tree Detection
 =============================
 
-*work in progress, move word docs to rst*
-
 This is the documentation page related to the GitHub repository: 
 `urban-tree-detection <https://github.com/NINAnor/urban-tree-detection>`_
 
@@ -42,12 +40,11 @@ Installation
 ------------
 .. toctree::
    :maxdepth: 1 
-
-   ../05_installation_manuals/01_tree_detection_installation
+   :caption: View the installation manual and project structure for instructions.
+
+   installation_manual
    project_structure
 
-
-
 Data
 ----
 
@@ -56,8 +53,8 @@ Data
 
 
 
-Workflow
-----------
+Methods
+-------
 1. **Create a study area mask** (*optional manual action*)
 
    We recommend to create a study area mask manually, as it is specific to each municipality

diff --git a/...manuals/01_tree_detection_installation.md → ...tree_detection/installation_manual.md.txt b/...manuals/01_tree_detection_installation.md → ...tree_detection/installation_manual.md.txt
@@ -1,8 +1,8 @@
-# Urban Tree Detection Installation Manual
+# Installation Manual | *urban-tree-detection*
 
-## Environment Setup and Configuration
+**GitHub Repository**: [urban-tree-detection](https://github.com/NINAnor/urban-tree-detection)
 
-### Installation 
+## Installation 
 
 The code runs in an ArcGIS Pro 3.1.0. conda environment and depends on 3D analyst, image analyst, spatial analyst licenses. 
 
@@ -32,7 +32,7 @@ Here are the steps to create a conda env compatible with ArcGIS Pro 3.0.1 and to
         # verify name is deleted from list
         conda info --envs
 
-4.  Install linters using pipx 
+4.  (Optional) Install linters using pipx 
     ```bash
         # install linters using make
         make install-global
@@ -42,7 +42,7 @@ Here are the steps to create a conda env compatible with ArcGIS Pro 3.0.1 and to
 
     **note:** As `pre-commit` unfortunately gives acces-denied errors on Windows OS, I would recommend to run `make codestyle` command before you commit your changes. This command runs black, isort and ruff on all files.
 
-### Configuration
+## Configuration
 This project uses a .env and a config.yaml file to store configuration variables. The module `utils.config.py` and `yaml_utils.py` provides functions to read and write these files.
 
 Run `src/test/test_config.py` to test the configuration and logger.

diff --git a/docs/html/_sources/methods/01_tree_detection/project_structure.md.txt b/docs/html/_sources/methods/01_tree_detection/project_structure.md.txt
@@ -1,9 +1,12 @@
 
-# Project Structure
+# Project Structure | *urban-tree-detection*
 
+**GitHub Repository**: [urban-tree-detection](https://github.com/NINAnor/urban-tree-detection)
 
 ## Project folder structure
 
+**TODO** CHECK AND UPDATE PROJECT FOLDER STRUCTURE
+
 ```bash
 C:\path\to\project\folder	
 ├── .gitignore

diff --git a/docs/html/_sources/methods/02_support_tools/README.rst.txt b/docs/html/_sources/methods/02_support_tools/README.rst.txt
@@ -0,0 +1,44 @@
+==============================
+Task X | Title
+==============================
+
+This repository provides a workflow for ...
+
+Code is provided for the following tasks:
+
+1. **Tekst here :** ...
+
+2. **Tekst here:** ...   
+
+The repository is applied on the Norwegian municipalities: *Bærum, Bodø, Kristiansand* and *Oslo.* 
+
+
+Installation
+------------
+.. toctree::
+   :maxdepth: 1 
+   :caption: View the installation manual and project structure for instructions.
+
+   installation_manual
+   project_structure
+
+
+
+Data
+----
+
+
+Methods
+-------
+
+
+**References**
+
+- ref here
+- ref here
+
+**Contributors**
+
+- Willeke A'Campo (NINA), [email protected]
+
+
diff --git a/docs/html/_sources/methods/02_support_tools/README_integration.md.txt b/docs/html/_sources/methods/02_support_tools/README_integration.md.txt
@@ -1,14 +1,14 @@
-# Task 2 | Integration of Municipal Tree Data and ALS Data
+# Task 2 | Integration of Municipal Tree points and Laser-detected Tree Crown polygons
 
-This repository provides a workflow for preparing municipal tree data for i-Tree Eco analysis and extrapolating the results to full the study area extent, using lidar-segmented tree crowns and auxiliary GIS datasets.
+This repository provides a workflow for preparing municipal tree data for i-Tree Eco analysis and extrapolating the results to full the study area extent, using the lidar-segmented tree crowns and auxiliary GIS datasets.
 
 ------------
 
 Code is provided for the following tasks:
 
 1. **i-Tree Eco Data Preparation:** preparing an input dataset for i-Tree Eco analysis by supplementing existing municipal tree inventories with crown geometry from the ALS data and auxiliary spatial datasets following the workflow by *Cimburova and Barton (2020).*  
 
-2. **i-Tree Eco Extrapolation:** extrapolating the outputs from i-Tree Eco analysis to all trees in the study area following the workflow by Cimburova and Barton (2020).    
+2. **i-Tree Eco Extrapolation:** extrapolating the outputs from i-Tree Eco analysis to all trees in the study area.    
 
 The repository is applied on the Norwegian municipalities: *Bærum, Bodø, Kristiansand* and *Oslo.* 
 
@@ -17,49 +17,7 @@ The repository is applied on the Norwegian municipalities: *Bærum, Bodø, Krist
 
 
 
-## Project Installation and Configuration
 
-The code is build in an ArcGIS Pro 3.1.0. conda environment with the spatial analyst license enabled. 
-
-1. Clone the repository.
-3. Open [Project structure](docs/project_structure.md) to view the structure of the project.
-4. Set up your Python Environment:
-
-    a. Create a new conda environment using the `environment.yml` file or clone the arcgispro-py3 environment from your ArcGIS Pro installation and install the required packages listed in the `requirements.txt` file.
-    ```bash
-        cd path/to/project/folder
-        conda env create -f environment.yml
-        conda activate project-name
-    ```
-
-    b. (Optional) Install linters using pipx 
-    ```bash
-        # install linters using pipx
-        make install-global
-        # test linters
-        make codestyle
-    ```
-
-    **note:** As `pre-commit` unfortunately often gives acces-denied errors on Windows OS, I would recommend to run `make codestyle` command before you commit your changes. This command runs black, isort and ruff on all files using the configuration specified in the [pyproject.toml](pyproject.toml) file.
-
-    c. Install as a local package 
-    ```bash
-        pip install .
-        pip install -e . # for development
-    ```
-    -  installs project packages in development mode
-    - creates a folder **package-name.egg-info**
-
-    d. Configure your project. 
-
-    - Copy template.env to  $user/.env and fill in the variables. 
-    *ENSURE THAT YOU DO NOT COMMIT .ENV TO THE REPOSITORY*
-    - check that your data is located in the correct folders, look at the [Project structure](docs/project_structure.md) and the [Catalog](config/catalog.yaml) for more details. 
-
-    e. Define your municipality in the [parameters](config/parameters.yaml) file.
-
-    d. Run `config.py` in the conda env to test your project config.
--------
 
 ## Workflow | i-Tree Eco Data Preparation
 

diff --git a/docs/html/_sources/methods/02_support_tools/installation_manual.md.txt b/docs/html/_sources/methods/02_support_tools/installation_manual.md.txt
@@ -0,0 +1,48 @@
+# Installation Manual | *itree-support-tools*
+
+**GitHub Repository**: [itree-support-tools](https://github.com/NINAnor/itree-support-tools)
+
+## Installation
+
+The code is build in an ArcGIS Pro 3.1.0. conda environment with the spatial analyst license enabled. 
+
+1. Clone the repository.
+3. Open [Project structure](project_structure.md) to view the structure of the project.
+4. Set up your Python Environment:
+
+    a. Create a new conda environment using the `environment.yml` file or clone the arcgispro-py3 environment from your ArcGIS Pro installation and install the required packages listed in the `requirements.txt` file.
+    ```bash
+        cd path/to/project/folder
+        conda env create -f environment.yml
+        conda activate project-name
+    ```
+
+    b. (Optional) Install linters using pipx 
+    ```bash
+        # install linters using pipx
+        make install-global
+        # test linters
+        make codestyle
+    ```
+
+    **note:** As `pre-commit` unfortunately often gives acces-denied errors on Windows OS, I would recommend to run `make codestyle` command before you commit your changes. This command runs black, isort and ruff on all files using the configuration specified in the [pyproject.toml](pyproject.toml) file.
+
+    c. Install as a local package 
+    ```bash
+        pip install .
+        pip install -e . # for development
+    ```
+    -  installs project packages in development mode
+    - creates a folder **package-name.egg-info**
+
+## Configuration
+
+1. Copy template.env to  $user/.env and fill in the variables. 
+*ENSURE THAT YOU DO NOT COMMIT .ENV TO THE REPOSITORY*
+
+2. Check that your data is located in the correct folders, look at the [Project structure](docs/project_structure.md) and the [Catalog](config/catalog.yaml) for more details. 
+
+3. Define your municipality in the [parameters](config/parameters.yaml) file.
+
+4. Run `config.py` in the conda env to test your project config.
+-------
diff --git a/docs/html/_sources/methods/02_support_tools/project_structure.md.txt b/docs/html/_sources/methods/02_support_tools/project_structure.md.txt
@@ -1,5 +1,11 @@
 
-# Project Structure
+# Project Structure | *itree-support-tools*
+
+**GitHub Repository**: [itree-support-tools](https://github.com/NINAnor/itree-support-tools)
+
+## Project folder structure
+
+**TODO** CHECK AND UPDATE PROJECT FOLDER STRUCTURE
 
 ```bash
 C:\path\to\project\folder	
@@ -55,4 +61,22 @@ The following files are included in this template:
     - [utils.py](src/utils.py) project utility methods.
     - [decorators.py](src/decorators.py) project decorators.
 
--------
+-------
+
+
+## Data folder structure
+Data is organized by municipality and has a similar sub-folder structure for each municipality. The data folder contains the following sub-folders:
+
+```shell
+path/to/urban-tree-detection/
+    ├── data
+    │   ├── bodo
+    │   │   ├── interim        <- Intermediate data that has been transformed.
+    │   │   ├── processed      <- The final, canonical data sets for modeling.
+    │   │   └── raw            <- The original, immutable data dump.
+    │   ├── baerum
+    │   ├── kristiansand
+    │   └── oslo
+    ├── ...
+    └── ...
+```