openforis-whisp 2.0.0a3__tar.gz → 2.0.0a4__tar.gz

{openforis_whisp-2.0.0a3 → openforis_whisp-2.0.0a4}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.3
 Name: openforis-whisp
-Version: 2.0.0a3
+Version: 2.0.0a4
 Summary: Whisp (What is in that plot) is an open-source solution which helps to produce relevant forest monitoring information and support compliance with deforestation-related regulations.
 License: MIT
 Keywords: whisp,geospatial,data-processing
@@ -59,7 +59,6 @@ Description-Content-Type: text/markdown
   - [Whisp pathways](#whisp_pathways)
   - [Whisp datasets](#whisp_datasets)
   - [Whisp notebooks](#whisp_notebooks)
-  - [System setup](#whisp_setup)
   - [Add data layers](#whisp_add_data)
   - [Contribute to the code](#whisp_contribute)
   - [Code of conduct](#whisp_conduct)
@@ -176,7 +175,7 @@ The **relevant risk assessment column depends on the commodity** in question:
   10) Were there commodity plantations or other agricultural uses in 2023?
   11) Were there logging concessions?
 
-  # Run Whisp python package from a notebook
+  # Run Whisp python package from a notebook <a name="whisp_notebooks"></a>
 
   For most users we suggest using the Whisp App to process their plot data. But for some, using the python package directly will fit their workflow.
 
@@ -190,6 +189,7 @@ The **relevant risk assessment column depends on the commodity** in question:
 
   More info on Whisp can be found in [here](https://openknowledge.fao.org/items/e9284dc7-4b19-4f9c-b3e1-e6c142585865)
 
+
   ## Python package installation
 
   The Whisp package is available on pip
@@ -202,15 +202,15 @@ The **relevant risk assessment column depends on the commodity** in question:
   pip install --pre openforis-whisp
   ```
 
-  If running locally we recommend a [virtual environment](https://docs.python.org/3/library/venv.html) to keep your main python installation clean.
+  If running the package locally we recommend a [virtual environment](https://docs.python.org/3/library/venv.html) to keep your main python installation clean. For users running the package in Sepal see [here](https://docs.sepal.io/en/latest/cli/python.html#virtual-environment).
 
   The package relies upon the google earth engine api being setup correctly using a registered cloud project.
 
-  More info on Whisp can be found in [here](https://openknowledge.fao.org/items/e9284dc7-4b19-4f9c-b3e1-e6c142585865)
+  More info on Whisp can be found [here](https://openknowledge.fao.org/items/e9284dc7-4b19-4f9c-b3e1-e6c142585865)
 
 
 
-## How to add data layers to Whisp
+## How to add data layers to Whisp <a name="whisp_add_data"></a>
 
 
 
@@ -253,12 +253,24 @@ Before submitting a request, consider the following:
 ### Adding your own data directly
 
 
-
 To add your own data you will need some coding experience as well as familiarity with GitHub and Google Earth Engine.
 
+This approach is for those who want to run a bespoke analysis combining their own data with those already in Whisp.
+
+Firstly follow the steps below to install the package in editable mode.
 
-Firstly follow the steps to install the package in editable mode (as detailed below in Contributing to the Whisp code base). Once in editable mode you are running the Whisp package locally based on a cloned version of the code. This approach is for those who want to run a bespoke analysis combining their own data with those already in Whisp. If, however, you think the datasets are of use to the wider community and you have the code running smoothly, you can make a pull request from a forked repository. 
+As with the regular pip installation, we recommend a separate [virtual environment](https://docs.python.org/3/library/venv.html) for running in editable mode. For Sepal users see [here](https://docs.sepal.io/en/latest/cli/python.html#virtual-environment).
 
+```bash
+
+git  clone  https://github.com/forestdatapartnership/whisp.git
+
+cd  whisp/
+
+pip  install  -e  .[dev]
+
+```
+Once in editable mode you are running the Whisp package locally based on a cloned version of the code.
 
 
 
@@ -294,7 +306,7 @@ For example, if it is a dataset for tree cover in 2000, then add `'treecover'` u
 
 ```python
 
-def  nBR_my_custom_dataset_prep():
+def  my_custom_dataset_prep():
 
 image = ee.Image("MY/GEE/DATASET")
 
@@ -309,7 +321,6 @@ return binary.rename("My_custom_dataset")
 ---
 
 
-
 We are working on ways to make this process smoother. However, in the meantime do contact us through the [issues page on GitHub](https://github.com/forestdatapartnership/whisp/issues), or via the Open Foris email, if this functionality is useful to you or you need help.
 
 
@@ -318,28 +329,14 @@ We are working on ways to make this process smoother. However, in the meantime d
 
 
 
-## Contributing to the Whisp code base
-
+## Contributing to the Whisp code base <a name="whisp_contribute"></a>
 
+Contributions to the Whisp code in GitHub are welcome. These could be additional functionality, datasets or just cleaner code! Contributions can be made by forking the repository, making and pushing the required changes, then making a pull request to the Whisp repository. After briefly reviewing the request, we can make a branch for which to make a new pull request to. After final checks, we can then incorporate the code into the main branch. If in doubt, get in contact first or log as an issue [here](https://github.com/forestdatapartnership/whisp/issues/).
 
-Contributions to the Whisp code in GitHub are welcome. They can be made by forking the repository, making and pushing the required changes, then making a pull request to the Whisp repository. After briefly reviewing the request, we can make a branch for which to make a new pull request to. After final checks, we can then incorporate the code into the main branch. If in doubt, get in contact first or log as an issue [here](https://github.com/forestdatapartnership/whisp/issues/).
 
+Install the package in editable mode (see Adding your own data directly above):
 
-
-Install the package in editable mode:
-
-
-```bash
-
-git  clone  https://github.com/forestdatapartnership/whisp.git
-
-cd  whisp/
-
-pip  install  -e  .[dev]
-
-```
-
-Add additional dependencies required for testing and running pre-commit hooks:
+Then add additional dependencies required for testing and running pre-commit hooks:
 
 
 ```bash
@@ -352,7 +349,6 @@ pre-commit  install
 You should be able to run the Pytest suite by simply running the `pytest` command from the repo's root folder.
 
 
-
 Please read the [contributing guidelines](contributing_guidelines.md) for good practice recommendations
 
 

{openforis_whisp-2.0.0a3 → openforis_whisp-2.0.0a4}/README.md

@@ -22,7 +22,6 @@
   - [Whisp pathways](#whisp_pathways)
   - [Whisp datasets](#whisp_datasets)
   - [Whisp notebooks](#whisp_notebooks)
-  - [System setup](#whisp_setup)
   - [Add data layers](#whisp_add_data)
   - [Contribute to the code](#whisp_contribute)
   - [Code of conduct](#whisp_conduct)
@@ -139,7 +138,7 @@ The **relevant risk assessment column depends on the commodity** in question:
   10) Were there commodity plantations or other agricultural uses in 2023?
   11) Were there logging concessions?
 
-  # Run Whisp python package from a notebook
+  # Run Whisp python package from a notebook <a name="whisp_notebooks"></a>
 
   For most users we suggest using the Whisp App to process their plot data. But for some, using the python package directly will fit their workflow.
 
@@ -153,6 +152,7 @@ The **relevant risk assessment column depends on the commodity** in question:
 
   More info on Whisp can be found in [here](https://openknowledge.fao.org/items/e9284dc7-4b19-4f9c-b3e1-e6c142585865)
 
+
   ## Python package installation
 
   The Whisp package is available on pip
@@ -165,15 +165,15 @@ The **relevant risk assessment column depends on the commodity** in question:
   pip install --pre openforis-whisp
   ```
 
-  If running locally we recommend a [virtual environment](https://docs.python.org/3/library/venv.html) to keep your main python installation clean.
+  If running the package locally we recommend a [virtual environment](https://docs.python.org/3/library/venv.html) to keep your main python installation clean. For users running the package in Sepal see [here](https://docs.sepal.io/en/latest/cli/python.html#virtual-environment).
 
   The package relies upon the google earth engine api being setup correctly using a registered cloud project.
 
-  More info on Whisp can be found in [here](https://openknowledge.fao.org/items/e9284dc7-4b19-4f9c-b3e1-e6c142585865)
+  More info on Whisp can be found [here](https://openknowledge.fao.org/items/e9284dc7-4b19-4f9c-b3e1-e6c142585865)
 
 
 
-## How to add data layers to Whisp
+## How to add data layers to Whisp <a name="whisp_add_data"></a>
 
 
 
@@ -216,12 +216,24 @@ Before submitting a request, consider the following:
 ### Adding your own data directly
 
 
-
 To add your own data you will need some coding experience as well as familiarity with GitHub and Google Earth Engine.
 
+This approach is for those who want to run a bespoke analysis combining their own data with those already in Whisp.
+
+Firstly follow the steps below to install the package in editable mode.
 
-Firstly follow the steps to install the package in editable mode (as detailed below in Contributing to the Whisp code base). Once in editable mode you are running the Whisp package locally based on a cloned version of the code. This approach is for those who want to run a bespoke analysis combining their own data with those already in Whisp. If, however, you think the datasets are of use to the wider community and you have the code running smoothly, you can make a pull request from a forked repository. 
+As with the regular pip installation, we recommend a separate [virtual environment](https://docs.python.org/3/library/venv.html) for running in editable mode. For Sepal users see [here](https://docs.sepal.io/en/latest/cli/python.html#virtual-environment).
 
+```bash
+
+git  clone  https://github.com/forestdatapartnership/whisp.git
+
+cd  whisp/
+
+pip  install  -e  .[dev]
+
+```
+Once in editable mode you are running the Whisp package locally based on a cloned version of the code.
 
 
 
@@ -257,7 +269,7 @@ For example, if it is a dataset for tree cover in 2000, then add `'treecover'` u
 
 ```python
 
-def  nBR_my_custom_dataset_prep():
+def  my_custom_dataset_prep():
 
 image = ee.Image("MY/GEE/DATASET")
 
@@ -272,7 +284,6 @@ return binary.rename("My_custom_dataset")
 ---
 
 
-
 We are working on ways to make this process smoother. However, in the meantime do contact us through the [issues page on GitHub](https://github.com/forestdatapartnership/whisp/issues), or via the Open Foris email, if this functionality is useful to you or you need help.
 
 
@@ -281,28 +292,14 @@ We are working on ways to make this process smoother. However, in the meantime d
 
 
 
-## Contributing to the Whisp code base
-
+## Contributing to the Whisp code base <a name="whisp_contribute"></a>
 
+Contributions to the Whisp code in GitHub are welcome. These could be additional functionality, datasets or just cleaner code! Contributions can be made by forking the repository, making and pushing the required changes, then making a pull request to the Whisp repository. After briefly reviewing the request, we can make a branch for which to make a new pull request to. After final checks, we can then incorporate the code into the main branch. If in doubt, get in contact first or log as an issue [here](https://github.com/forestdatapartnership/whisp/issues/).
 
-Contributions to the Whisp code in GitHub are welcome. They can be made by forking the repository, making and pushing the required changes, then making a pull request to the Whisp repository. After briefly reviewing the request, we can make a branch for which to make a new pull request to. After final checks, we can then incorporate the code into the main branch. If in doubt, get in contact first or log as an issue [here](https://github.com/forestdatapartnership/whisp/issues/).
 
+Install the package in editable mode (see Adding your own data directly above):
 
-
-Install the package in editable mode:
-
-
-```bash
-
-git  clone  https://github.com/forestdatapartnership/whisp.git
-
-cd  whisp/
-
-pip  install  -e  .[dev]
-
-```
-
-Add additional dependencies required for testing and running pre-commit hooks:
+Then add additional dependencies required for testing and running pre-commit hooks:
 
 
 ```bash
@@ -315,7 +312,6 @@ pre-commit  install
 You should be able to run the Pytest suite by simply running the `pytest` command from the repo's root folder.
 
 
-
 Please read the [contributing guidelines](contributing_guidelines.md) for good practice recommendations
 
 

{openforis_whisp-2.0.0a3 → openforis_whisp-2.0.0a4}/pyproject.toml

@@ -4,7 +4,7 @@ build-backend = "poetry.core.masonry.api"
 
 [tool.poetry]
 name = "openforis-whisp"
-version = "2.0.0a3"
+version = "2.0.0a4"
 description = "Whisp (What is in that plot) is an open-source solution which helps to produce relevant forest monitoring information and support compliance with deforestation-related regulations."
 repository = "https://github.com/forestdatapartnership/whisp"
 authors = ["Andy Arnell <and.arnell@fao.org>"]

{openforis_whisp-2.0.0a3 → openforis_whisp-2.0.0a4}/src/openforis_whisp/datasets.py

@@ -58,19 +58,6 @@ def g_jrc_gfc_2020_prep():
     return jrc_gfc2020_raw.mosaic().rename("EUFO_2020")
 
 
-## removing JAXA product due to repeat errors of commission being noted by users, compared to other datasets
-
-# # JAXA_FNF_2020
-# def g_jaxa_forest_prep():
-#     jaxa_forest_non_forest_raw = ee.ImageCollection("JAXA/ALOS/PALSAR/YEARLY/FNF4")
-#     jaxa_forest_non_forest_2020 = (
-#         jaxa_forest_non_forest_raw.filterDate("2020-01-01", "2020-12-31")
-#         .select("fnf")
-#         .mosaic()
-#     )
-#     return jaxa_forest_non_forest_2020.lte(2).rename("JAXA_FNF_2020")
-
-
 # GFC_TC_2020
 def g_glad_gfc_10pc_prep():
     gfc = ee.Image("UMD/hansen/global_forest_change_2024_v1_12")
@@ -285,7 +272,7 @@ def g_fdap_rubber_2023_prep():
     fdap_rubber = (
         fdap_rubber2020_model_raw.filterDate("2023-01-01", "2023-12-31")
         .mosaic()
-        .gt(0.93)  # Threshold for Rubber
+        .gt(0.59)  # Threshold for Rubber
     )
     return fdap_rubber.rename("Rubber_2023_FDaP")
 

{openforis_whisp-2.0.0a3 → openforis_whisp-2.0.0a4}/src/openforis_whisp/parameters/lookup_gee_datasets.csv

@@ -2,7 +2,6 @@ name,order,ISO2_code,theme,theme_timber,use_for_risk,use_for_risk_timber,exclude
 EUFO_2020,10,,treecover,naturally_reg_2020,1,1,0,float32,1,0,g_jrc_gfc_2020_prep
 GLAD_Primary,20,,treecover,primary,1,1,0,float32,1,0,g_glad_pht_prep
 TMF_undist,30,,treecover,primary,1,1,0,float32,1,0,g_jrc_tmf_undisturbed_prep
-JAXA_FNF_2020,40,,treecover,NA,1,0,1,float32,1,0,g_jaxa_forest_prep
 GFC_TC_2020,50,,treecover,naturally_reg_2020,1,1,0,float32,1,0,g_glad_gfc_10pc_prep
 Forest_FDaP,60,,treecover,naturally_reg_2020,1,1,0,float32,1,0,g_glad_gfc_10pc_prep
 ESA_TC_2020,70,,treecover,naturally_reg_2020,1,1,0,float32,1,0,g_esa_worldcover_trees_prep
@@ -173,7 +172,7 @@ ESRI_2023_crop,2130,,NA,agri_after_2020,0,1,0,float32,1,0,g_esri_2023_crop_prep
 GLC_FCS30D_crop_2022,2140,,NA,agri_after_2020,0,1,0,float32,1,0,g_glc_fcs30d_crop_2022_prep
 GFW_logging_before_2020,2200,,NA,logging_concession,0,1,0,float32,1,0,g_logging_concessions_prep
 nCO_ideam_forest_2020,2310,CO,treecover,NA,1,1,0,float32,1,0,nco_ideam_forest_2020_prep
-nCO_ideam_eufo_commission_2020,2320,CO,commodities,NA,0,1,0,float32,1,0,nco_ideam_eufo_commission_2020_prep
+nCO_ideam_eufo_commission_2020,2320,CO,commodities,NA,1,1,0,float32,1,0,nco_ideam_eufo_commission_2020_prep
 nBR_INPE_TC_primary_forest_Amazon_2020,2400,BR,treecover,primary,1,1,0,float32,1,0,nbr_terraclass_amz20_primary_prep
 nBR_INPE_TC_secondary_forest_Amazon_2020,2401,BR,treecover,naturally_reg_2020,1,1,0,float32,1,0,nbr_terraclass_amz20_secondary_prep
 nBR_BFS_primary_forest_Pantanal_2020,2402,BR,treecover,primary,1,1,0,float32,1,0,nbr_bfs_ptn_f20_prep