Merge c1a6d91 into 69a1044

.github/workflows/python-package.yml

@@ -29,21 +29,35 @@ jobs:
     - uses: actions/checkout@v2
 
     # Set up the conda-forge environment with mamba
-    - name: Set up Python ${{ matrix.python-version }} and dependencies
+    - name: Set up Python ${{ matrix.python-version }} and base environment
       uses: conda-incubator/setup-miniconda@v2
       with:
         auto-update-conda: true
         python-version: ${{ matrix.python-version }}
         mamba-version: "*"
         channels: conda-forge
         channel-priority: strict
-        environment-file: dev-environment.yml
-        activate-environment: xdem-dev
+        environment-file: environment.yml
+        activate-environment: xdem
 
     - name: Install project
       run: |
         pip install --no-dependencies --editable .
 
+    # This steps allows us to check the "import xdem" with the base environment provided to users, before adding
+    # development-specific dependencies by differencing the env and dev-env yml files
+    - name: Check normal environment import
+      run: |
+        python -c "import xdem"
+
+    - name: Update environment with dev dependencies
+      run: |
+        mamba env update --name xdem --file dev-environment.yml
+
+    - name: Re-install project
+      run: |
+        pip install -e . --no-dependencies
+
     - name: Lint with flake8
       run: |
         # stop the build if there are Python syntax errors or undefined names

dev-environment.yml

@@ -6,7 +6,6 @@ dependencies:
   - proj>=7.2
   - fiona
   - shapely
-  - autovizwidget
   - numba
   - numpy
   - matplotlib
@@ -16,12 +15,12 @@ dependencies:
   - scipy
   - tqdm
   - scikit-image
-  - richdem
   - proj-data
   - scikit-gstat>=0.6.8
   - pytransform3d
 
   # Development-specific
+  - autovizwidget
   - pytest
   - pytest-xdist
   - sphinx
@@ -31,6 +30,8 @@ dependencies:
   - flake8
   - sphinx-autodoc-typehints
   - sphinx-gallery
+  - pyyaml
+  - richdem
 
   - pip:
     - git+https://github.com/GlacioHack/geoutils.git

dev-requirements.txt

@@ -16,3 +16,4 @@ scikit-gstat
 flake8
 opencv-contrib-python
 sphinx-gallery
+pyyaml

environment.yml

@@ -18,4 +18,6 @@ dependencies:
   - proj-data
   - scikit-gstat>=0.6.8
   - pytransform3d
-  - geoutils>=0.0.8
+
+  - pip:
+      - git+https://github.com/GlacioHack/geoutils.git

tests/test_misc.py

@@ -1,6 +1,7 @@
 """Test the xdem.misc functions."""
 from __future__ import annotations
 
+import os
 import warnings
 
 import pytest
@@ -9,59 +10,94 @@
 import xdem.misc
 
 
-@pytest.mark.parametrize("deprecation_increment", [-1, 0, 1, None])  # type: ignore
-@pytest.mark.parametrize("details", [None, "It was completely useless!", "dunnowhy"])  # type: ignore
-def test_deprecate(deprecation_increment: int | None, details: str | None) -> None:
-    """
-    Test the deprecation warnings/errors.
-
-    If the removal_version is larger than the current, it should warn.
-    If the removal_version is smaller or equal, it should raise an error.
-
-    :param deprecation_increment: The version number relative to the current version.
-    :param details: An optional explanation for the description.
-    """
-    warnings.simplefilter("error")
-
-    current_version = xdem.version.version
-
-    # Set the removal version to be the current version plus the increment (e.g. 0.0.5 + 1 -> 0.0.6)
-    removal_version = (
-        current_version[:-1] + str(int(current_version.rsplit(".", 1)[1]) + deprecation_increment)
-        if deprecation_increment is not None
-        else None
-    )
-
-    # Define a function with no use that is marked as deprecated.
-    @xdem.misc.deprecate(removal_version, details=details)  # type: ignore
-    def useless_func() -> int:
-        return 1
-
-    # If True, a warning is expected. If False, a ValueError is expected.
-    should_warn = removal_version is None or removal_version > current_version
-
-    # Add the expected text depending on the parametrization.
-    text = (
-        "Call to deprecated function 'useless_func'."
-        if should_warn
-        else f"Deprecated function 'useless_func' was removed in {removal_version}."
-    )
-
-    if details is not None:
-        text += " " + details.strip().capitalize()
-
-        if not any(text.endswith(c) for c in ".!?"):
-            text += "."
-
-    if should_warn and removal_version is not None:
-        text += f" This functionality will be removed in version {removal_version}."
-    elif not should_warn:
-        text += f" Current version: {current_version}."
-
-    # Expect either a warning or an exception with the right text.
-    if should_warn:
-        with pytest.warns(DeprecationWarning, match="^" + text + "$"):
-            useless_func()
-    else:
-        with pytest.raises(ValueError, match="^" + text + "$"):
-            useless_func()
+import yaml  # type: ignore
+
+
+class TestMisc:
+    def test_environment_files(self) -> None:
+        """Check that environment yml files are properly written: all dependencies of env are also in dev-env"""
+
+        fn_env = os.path.abspath(os.path.join(os.path.dirname(__file__), "..", "environment.yml"))
+        fn_devenv = os.path.abspath(os.path.join(os.path.dirname(__file__), "..", "dev-environment.yml"))
+
+        # Load the yml as dictionaries
+        yaml_env = yaml.safe_load(open(fn_env))
+        yaml_devenv = yaml.safe_load(open(fn_devenv))
+
+        # Extract the dependencies values
+        conda_dep_env = yaml_env["dependencies"]
+        conda_dep_devenv = yaml_devenv["dependencies"]
+
+        # Check if there is any pip dependency, if yes pop it from the end of the list
+        if isinstance(conda_dep_devenv[-1], dict):
+            pip_dep_devenv = conda_dep_devenv.pop()
+
+            # Check if there is a pip dependency in the normal env as well, if yes pop it also
+            if isinstance(conda_dep_env[-1], dict):
+                pip_dep_env = conda_dep_env.pop()
+
+                # The diff below computes the dependencies that are in env but not in dev-env
+                # It should be empty, otherwise we raise an error
+                diff_pip_check = list(set(pip_dep_env) - set(pip_dep_devenv))
+                assert len(diff_pip_check) == 0
+
+        # We do the same for the conda dependency, first a sanity check that everything that is in env is also in dev-ev
+        diff_conda_check = list(set(conda_dep_env) - set(conda_dep_devenv))
+        assert len(diff_conda_check) == 0
+
+    @pytest.mark.parametrize("deprecation_increment", [-1, 0, 1, None])  # type: ignore
+    @pytest.mark.parametrize("details", [None, "It was completely useless!", "dunnowhy"])  # type: ignore
+    def test_deprecate(self, deprecation_increment: int | None, details: str | None) -> None:
+        """
+        Test the deprecation warnings/errors.
+
+        If the removal_version is larger than the current, it should warn.
+        If the removal_version is smaller or equal, it should raise an error.
+
+        :param deprecation_increment: The version number relative to the current version.
+        :param details: An optional explanation for the description.
+        """
+        warnings.simplefilter("error")
+
+        current_version = xdem.version.version
+
+        # Set the removal version to be the current version plus the increment (e.g. 0.0.5 + 1 -> 0.0.6)
+        removal_version = (
+            current_version[:-1] + str(int(current_version.rsplit(".", 1)[1]) + deprecation_increment)
+            if deprecation_increment is not None
+            else None
+        )
+
+        # Define a function with no use that is marked as deprecated.
+        @xdem.misc.deprecate(removal_version, details=details)  # type: ignore
+        def useless_func() -> int:
+            return 1
+
+        # If True, a warning is expected. If False, a ValueError is expected.
+        should_warn = removal_version is None or removal_version > current_version
+
+        # Add the expected text depending on the parametrization.
+        text = (
+            "Call to deprecated function 'useless_func'."
+            if should_warn
+            else f"Deprecated function 'useless_func' was removed in {removal_version}."
+        )
+
+        if details is not None:
+            text += " " + details.strip().capitalize()
+
+            if not any(text.endswith(c) for c in ".!?"):
+                text += "."
+
+        if should_warn and removal_version is not None:
+            text += f" This functionality will be removed in version {removal_version}."
+        elif not should_warn:
+            text += f" Current version: {current_version}."
+
+        # Expect either a warning or an exception with the right text.
+        if should_warn:
+            with pytest.warns(DeprecationWarning, match="^" + text + "$"):
+                useless_func()
+        else:
+            with pytest.raises(ValueError, match="^" + text + "$"):
+                useless_func()