Merge branch 'main' into rioxarray

.github/workflows/unit.yml

@@ -56,7 +56,7 @@ jobs:
       - name: Install nox
         run: python -m pip install nox
       - name: test with pytest
-        run: nox -s test
+        run: nox -s test -- -vv
       - name: codecov
         uses: codecov/codecov-action@v3
         with:

.gitignore

@@ -10,6 +10,8 @@ __pycache__/
 *$py.class
 *[Uu]ntitled*
 
+.github/workflows/act_unit.yml
+
 # C extensions
 *.so
 

.pre-commit-config.yaml

@@ -38,11 +38,11 @@ repos:
       - id: doc8
         stages: [commit]
 
-  - repo: https://github.com/FHPythonUtils/LicenseCheck
-    rev: "2023.1.1"
-    hooks:
-      - id: licensecheck
-        stages: [commit]
+  # - repo: https://github.com/FHPythonUtils/LicenseCheck
+  #   rev: "2023.1.1"
+  #   hooks:
+  #     - id: licensecheck
+  #       stages: [commit]
 
   - repo: https://github.com/codespell-project/codespell
     rev: v2.2.4

CONTRIBUTING.rst

@@ -218,3 +218,28 @@ We are using :code:`api-doc` to build the documentation of the lib so if you wan
     sphinx-apidoc --force --module-first --templatedir=docs/source/_templates/apidoc -o docs/source/modules
 
 You can then build the documentation, it will automatically call :code:`autodoc` and :code:`autosummary` during the process.
+
+
+Test the workflows locally
+--------------------------
+
+Test your locally your workflows using `Act <https://github.com/nektos/act>`_.
+
+To pass your secrets to the workflows, create a `secrets.env` file and store the secrets of your custom workflow, for example:
+
+.. code-block:: console
+
+    EARTHENGINE_TOKEN=""
+    PLANET_API_CREDENTIALS=""
+    PLANET_API_KEY=""
+    FIRMS_API_KEY=""
+    EARTHENGINE_SERVICE_ACCOUNT=""
+
+Then run the following command:
+
+.. code-block:: console
+
+    $ gh act --secret-file $ENV_FILE --workflows .github/workflows/unit.yml
+
+You can change the workflow file to test the one you want, if you are only interested in testing some specific jobs, you can use the `--job` flag.
+

docs/source/index.rst

@@ -44,4 +44,3 @@ Meet our :doc:`contributor <./start/authors>`.
     widgets/index
     API Content <modules/sepal_ui>
     cli/index
-    changelog

noxfile.py

@@ -19,6 +19,15 @@ def lint(session):
 def test(session):
     """Run all the test using the environment variable of the running machine."""
     session.install(".[test]")
+
+    # if we are in the sepal-venv, force earthengine api fork
+    if "sepal-user" in session.virtualenv.location:
+        session.run(
+            "pip",
+            "install",
+            "git+https://github.com/openforis/earthengine-api.git@v0.1.384#egg=earthengine-api&subdirectory=python",
+        )
+
     test_files = session.posargs or ["tests"]
     session.run("pytest", "--color=yes", "--cov", "--cov-report=xml", *test_files)
 

pyproject.toml

@@ -4,7 +4,7 @@ build-backend = "setuptools.build_meta"
 
 [project]
 name = "sepal-ui"
-version = "2.17.0"
+version = "2.20.0"
 description = "Wrapper for ipyvuetify widgets to unify the display of voila dashboards in SEPAL platform"
 keywords = ["UI", "Python", "widget", "sepal"]
 classifiers = [
@@ -36,7 +36,7 @@ dependencies = [
     "geopandas",
     "matplotlib",
     "jupyter-server-proxy", # required for localtileserver
-    "planet>=2",
+    "planet",
     "pyarrow",
     "localtileserver>=0.7.0", # first pure rio version
     "pygaul>=0.3.1", # use the class implementation
@@ -88,7 +88,7 @@ test = [
     "tomli",
 ]
 doc = [
-    "sphinx<7",
+    "sphinx @ git+https://github.com/sphinx-doc/sphinx.git",
     "jupyter-sphinx",
     "pydata-sphinx-theme",
     "sphinx-notfound-page",
@@ -97,6 +97,7 @@ doc = [
     "sphinxcontrib-autoprogram",
     "sphinx-favicon>=1.0.1",
     "tomli",
+    "lxml_html_clean",
 ]
 
 [project.scripts]
@@ -107,6 +108,7 @@ module_theme = "sepal_ui.bin.module_theme:main"
 module_venv = "sepal_ui.bin.module_venv:main"
 activate_venv = "sepal_ui.bin.activate_venv:main"
 sepal_ipyvuetify = "sepal_ui.bin.sepal_ipyvuetify:main"
+entry_point = "sepal_ui.bin.entry_point:main"
 
 [tool.setuptools]
 include-package-data = false
@@ -129,7 +131,7 @@ changelog_file = "CHANGELOG.md"
 changelog_incremental = true
 tag_format = "v$major.$minor.$patch$prerelease"
 update_changelog_on_bump = false
-version = "2.17.0"
+version = "2.20.0"
 version_files = [
     "pyproject.toml:version",
     "sepal_ui/__init__.py:__version__"

sepal_ui/__init__.py

@@ -10,7 +10,7 @@
 
 __author__ = """Pierrick Rambaud"""
 __email__ = "pierrick.rambaud49@gmail.com"
-__version__ = "2.17.0"
+__version__ = "2.20.0"
 
 color = SepalColor()
 'color: the colors of sepal. members are in the following list: "main, darker, bg, primary, accent, secondary, success, info, warning, error, menu". They will render according to the selected theme.'

sepal_ui/bin/entry_point.py

@@ -0,0 +1,65 @@
+#!/usr/bin/python3
+
+"""Script to rename the kernel of a notebook to a specific name."""
+
+import argparse
+import json
+from pathlib import Path
+
+from colorama import Fore, init
+
+init()
+
+# init parser
+parser = argparse.ArgumentParser(description=__doc__, usage="entry_point")
+
+parser.add_argument("file", help="UI file path")
+
+# Add a optional argument
+parser.add_argument("-t", "--test", help="Either test or not (production)", action="store_true")
+
+
+def main() -> None:
+    """Launch the venv creation process."""
+    # read arguments (there should be none)
+    args = parser.parse_args()
+
+    ui_file = args.file
+    test = args.test
+
+    # welcome the user
+    print(f"{Fore.YELLOW}UI renaming process{Fore.RESET}")
+
+    # check that the local folder is a module folder
+    ui_file = Path.cwd() / ui_file
+    if not ui_file.is_file():
+        raise Exception(f"{Fore.RED}This is not a module folder.")
+
+    entry_point = Path.cwd() / ui_file
+
+    # create the kernel from venv
+    prefix_name = "test-" if test else "venv-"
+    prefix_display = "(test) test-" if test else " (venv) "
+
+    name = f"{prefix_name}{Path.cwd().name}"
+    display_name = f"{prefix_display}{Path.cwd().name}"
+
+    # change the kernel of the entrypoint to use this one instead
+    with entry_point.open() as f:
+        data = json.load(f)
+
+    data["metadata"]["kernelspec"]["display_name"] = display_name
+    data["metadata"]["kernelspec"]["name"] = name
+
+    entry_point.write_text(json.dumps(data, indent=1))
+
+    # display last message to the end user
+    print(
+        f'{Fore.GREEN}The python kernel of {args.file} has been updated"{display_name}".{Fore.RESET}'
+    )
+
+    return
+
+
+if __name__ == "__main__":
+    main()

sepal_ui/bin/module_venv.py

@@ -23,15 +23,16 @@
 
 # init parser
 parser = argparse.ArgumentParser(description=__doc__, usage="module_venv")
+parser.add_argument("--venv_prefix", default="test", help="Prefix for the virtual environment name")
 
 
 def main() -> None:
     """Launch the venv creation process."""
     # read arguments (there should be none)
-    parser.parse_args()
+    args = parser.parse_args()
 
     # welcome the user
-    print(f"{Fore.YELLOW}venv creation interface{Fore.RESET}")
+    print(f"{Fore.YELLOW}venv creation interface v10{Fore.RESET}")
 
     # check that the local folder is a module folder
     ui_file = Path.cwd() / "ui.ipynb"
@@ -63,12 +64,52 @@ def main() -> None:
     pip = current_dir_venv / "bin" / "pip"
     python3 = current_dir_venv / "bin" / "python3"
 
-    for lib in ["wheel", "Cython", "ipykernel"]:
-        subprocess.run([str(pip), "install", lib], cwd=Path.cwd())
+    base_libs = ["wheel", "ipykernel", "numpy"]
+
+    # if we are in sepal, install earthengine-api OF fork
+
+    if "sepal-user" in str(Path.cwd()):
+        earthengine_api = "git+https://github.com/openforis/earthengine-api.git@v0.1.384#egg=earthengine-api&subdirectory=python"
+        base_libs.append(earthengine_api)
+
+    subprocess.run([str(pip), "install", "--upgrade", "pip"], cwd=Path.cwd())
+
+    for lib in base_libs:
+        subprocess.run([str(pip), "install", "--no-cache-dir", lib], cwd=Path.cwd())
+
+    # Default installation of GDAL
+    # If we are installing it as venv (usually in github actions) we need to install gdal as binary
+    gdal_version = "3.8.3"
+
+    # We assume we are in a github action runner if the path contains "home/runner/"
+    if "home/runner/" not in str(Path.cwd()):
+        subprocess.run(
+            [str(pip), "install", "--no-cache-dir", f"GDAL=={gdal_version}"], cwd=Path.cwd()
+        )
+    else:
+        subprocess.run(
+            [
+                str(pip),
+                "install",
+                "--no-cache-dir",
+                "--find-links=https://girder.github.io/large_image_wheels",
+                f"GDAL=={gdal_version}",
+            ],
+            cwd=Path.cwd(),
+        )
 
     # install all the requirements
     req = Path.cwd() / "requirements.txt"
-    subprocess.run([str(pip), "install", "-r", str(req)], cwd=Path.cwd())
+    subprocess.run(
+        [
+            str(pip),
+            "install",
+            "--no-cache-dir",
+            "-r",
+            str(req),
+        ],
+        cwd=Path.cwd(),
+    )
 
     # search for the module.yaml file
     # it embeds name and entry point
@@ -82,11 +123,11 @@ def main() -> None:
 
     else:
         entry_point = Path.cwd() / "ui.ipynb"
-        name = Path.cwd().stem
+        name = Path.cwd().name
 
     # create the kernel from venv
-    name = f"test-{Path.cwd().stem}"
-    display_name = f"(test) {name}"
+    name = f"{args.venv_prefix}-{Path.cwd().name}"
+    display_name = f"({args.venv_prefix}) {name}"
     subprocess.run(
         [
             str(python3),

sepal_ui/frontend/css/custom.css

@@ -31,6 +31,7 @@ header.v-app-bar {
 /* set the menu_content on top of the map when it's set to fullscreen */
 .v-menu__content {
   max-width: 100% !important;
+  z-index: 801 !important;
 }
 
 /* make sure navigation drawers are always visible when they exist */

sepal_ui/message/ar-SA/decorator.json

@@ -0,0 +1,6 @@
+{
+  "decorator": {
+    "no_alert": "",
+    "no_button": ""
+  }
+}