modified: .zenodo.json

	modified:   CHANGELOG.md
	modified:   MANIFEST.in
	modified:   README.md
	modified:   docker/initialize.py
	modified:   docs/source/conf.py
	modified:   docs/source/index.rst
	modified:   docs/source/install.rst
	modified:   docs/source/r-install.rst
	new file:   geoenrich/data/personal_catalog.csv
	modified:   geoenrich/satellite.py
	modified:   setup.cfg

Author: morand-g

.zenodo.json

@@ -13,7 +13,7 @@
 
     "license": "GPL-3.0",
 
-    "title": "GeoEnrich v0.5.6: a new tool for scientists to painlessly enrich species occurrence data with environmental variables",
+    "title": "GeoEnrich v0.5.7: a new tool for scientists to painlessly enrich species occurrence data with environmental variables",
 
     "related_identifiers": [
         {

CHANGELOG.md

@@ -1,3 +1,10 @@
+## v0.5.7
+
+#### New functions:
+- Added support for a *personal_catalog* file for a reliable use of user-defined datasets (see installation instructions).
+- Updated Docker image accordingly.
+- Added support for OpenMPI into the Docker image to enable parallel computing (Only to be used for separate points & separate variables, otherwise data loss will occur).
+
 ## v0.5.6
 
 #### New functions:

MANIFEST.in

@@ -1,4 +1,5 @@
 include geoenrich/data/AcDigitifera.zip
 include geoenrich/data/catalog.csv
+exclude geoenrich/personal_catalog.csv
 include geoenrich/data/areas.csv
 exclude geoenrich/credentials.py

README.md

@@ -1,4 +1,4 @@
-# **geoenrich 0.5.6**
+# **geoenrich 0.5.7**
 
 [![Read the Docs](https://img.shields.io/readthedocs/geoenrich)](https://geoenrich.readthedocs.io/en/latest/)
 [![License](https://img.shields.io/github/license/morand-g/geoenrich?color=green)](https://github.com/morand-g/geoenrich/blob/main/LICENSE)

docker/initialize.py

@@ -55,4 +55,7 @@
 if Path('/app/conf/credentials.py').exists():
     shutil.copy(Path('/app/conf/credentials.py'), Path('/usr/local/lib/python3.8/site-packages/geoenrich/credentials.py'))
 
+if Path('/app/conf/personal_catalog.csv').exists():
+    shutil.copy(Path('/app/conf/personal_catalog.csv'), Path('/usr/local/lib/python3.8/site-packages/geoenrich/data/personal_catalog.csv'))
+
 print('Initialization complete.')

docs/source/conf.py

@@ -25,7 +25,7 @@
 author = 'Gaétan Morand (UMR Marbec)'
 
 # The full version, including alpha/beta/rc tags
-release = '0.5.6'
+release = '0.5.7'
 
 
 # -- General configuration ---------------------------------------------------

docs/source/index.rst

@@ -1,4 +1,4 @@
-geoenrich 0.5.6 documentation
+geoenrich 0.5.7 documentation
 ==============================
 
 |Read the Docs| |License| |PyPI| |Python versions| |Last commit| |DOI|

docs/source/install.rst

@@ -42,20 +42,14 @@ There is also a dictionary named *dap_creds* that is intended to store credentia
 
 At the same location, there is a *catalog.csv* file that already contains a list of available variables. If you want to use a dataset from Copernicus, you first need to register on `their website <https://resources.marine.copernicus.eu/registration-form>`_ and write your credentials in the *credentials.py* file.
 
-If you need additional variables, you can update the *catalog.csv* file to add other opendap servers. Three columns are compulsory:
+If you need additional variables, you can update add a *personal_catalog.csv* file to the same folder (template on `GitHub <https://github.com/morand-g/geoenrich/blob/main/geoenrich/data/personal_catalog.csv>`_). Three columns are compulsory:
 
-- *variable*: A unique name for that variable (user defined).
+- *variable*: A unique name for that variable (user defined). It needs to be different from the variable names already in the built-in catalog.
 - *url*: OpenDAP URL.
 - *varname*: Name of the variable in the remote dataset.
 
 
-5. Precautions
---------------
-
-If you edited the *catalog.csv* file to add variables, you should make a backup of it, as it will get overwritten if you update or reinstall this package.
-
-
-5. Using the package
+6. Using the package
 --------------------
 
 Congrats, you can now use the `tutorial <https://geoenrich.readthedocs.io/en/latest/tutorial.html>`_ and start doing science!

docs/source/r-install.rst

@@ -54,20 +54,14 @@ There is also a dictionary named *dap_creds* that is intended to store credentia
 
 At the same location, there is a *catalog.csv* file that already contains a list of available variables. If you want to use a dataset from Copernicus, you first need to register on `their website <https://resources.marine.copernicus.eu/registration-form>`_ and write your credentials in the *credentials.py* file.
 
-If you need additional variables, you can update the *catalog.csv* file to add other opendap servers. Three columns are compulsory:
+If you need additional variables, you can update add a *personal_catalog.csv* file to the same folder (template on `GitHub <https://github.com/morand-g/geoenrich/blob/main/geoenrich/data/personal_catalog.csv>`_). Three columns are compulsory:
 
-- *variable*: A unique name for that variable (user defined).
+- *variable*: A unique name for that variable (user defined). It needs to be different from the variable names already in the built-in catalog.
 - *url*: OpenDAP URL.
 - *varname*: Name of the variable in the remote dataset.
 
 
-4. Precautions
---------------
-
-If you edited the *catalog.csv* file to add variables, you should make a backup of it, as it will get overwritten if you update or reinstall this package.
-
-
-5. Using the package
+4. Using the package
 --------------------
 
 Congrats, you can now use the `tutorial <https://geoenrich.readthedocs.io/en/latest/r-tutorial.html>`_ and start doing science!

geoenrich/data/personal_catalog.csv

@@ -0,0 +1 @@
+variable,source,spatial_resolution,time_resolution,time_coverage,depth_levels,url,varname

geoenrich/satellite.py

@@ -122,6 +122,10 @@ def get_var_catalog():
     path = Path(geoenrich.__file__).parent
     var_catalog = pd.read_csv(path / 'data' / 'catalog.csv', index_col = 0).to_dict('index')
 
+    if (path / 'data' / 'personal_catalog.csv').exists():
+        pers_vars = pd.read_csv(path / 'data' / 'personal_catalog.csv', index_col = 0).to_dict('index')
+        var_catalog = {**var_catalog, **pers_vars}
+
     for v in var_catalog:
         var_catalog[v]['var_id'] = v
         for domain in dap_creds:

setup.cfg

@@ -1,6 +1,6 @@
 [metadata]
 name = geoenrich
-version = 0.5.6
+version = 0.5.7
 author = Gaétan Morand (UMR Marbec)
 author_email = gaetan.morand@ird.fr
 description = A package to enrich your geo-referenced data (e.g. species occurrences) with environmental data.