Merge branch 'main' into feature/plugins

Author: emlys

.github/workflows/release-part-1.yml

@@ -53,7 +53,24 @@ jobs:
           perl -0777 -i -pe \
               "s/Unreleased Changes\n------------------/..\n  Unreleased Changes\n  ------------------\n\n${HEADER}\n${UNDERLINE}/g" \
               HISTORY.rst
+
+      - name: Install dependencies
+        run: pip install rst2html5
+
+      - name: Generate changelog.html
+        run: rst2html5 HISTORY.rst workbench/changelog.html
+
+      - name: Update package.json version
+        uses: BellCubeDev/update-package-version-by-release-tag@v2
+        with:
+          version: ${{ inputs.version }}
+          package-json-path: workbench/package.json
+
+      - name: Commit updated HISTORY.rst, changelog.html, and package.json
+        run: |
           git add HISTORY.rst
+          git add workbench/changelog.html
+          git add workbench/package.json
           git commit -m "Committing the $VERSION release."
 
       - name: Tag and push

.github/workflows/release-part-2.yml

@@ -99,7 +99,7 @@ jobs:
           twine upload \
             --username="__token__" \
             --password=${{ secrets.PYPI_NATCAP_INVEST_TOKEN }} \
-            artifacts/natcap.invest*
+            artifacts/natcap.invest* artifacts/natcap_invest*
 
       - name: Roll back on failure
         if: failure()

HISTORY.rst

@@ -44,13 +44,18 @@ Unreleased Changes
       ``pygeoprocessing.get_raster_info`` and
       ``pygeoprocessing.get_vector_info``.
       https://github.com/natcap/invest/issues/1645
-* Forest Carbon Edge Effects
-    * Updating vector reprojection to allow partial reprojection.  Related to
-      https://github.com/natcap/invest/issues/1645
-* Urban Nature Access
-    * The model now works as expected when the user provides an LULC raster
-      that does not have a nodata value defined.
-      https://github.com/natcap/invest/issues/1293
+    * The scripting page of the InVEST API documentation has been updated to
+      reflect changes in how InVEST is installed on modern systems, and also to
+      include images of the InVEST workbench instead of just broken links.
+      https://github.com/natcap/invest/issues/1660
+    * Updated translations for Spanish and Chinese
+    * natcap.invest now works with (and requires) ``gdal.UseExceptions``. A
+      ``FutureWarning`` is raised on import if GDAL exceptions are not enabled.
+    * Fixed an issue on Windows where GDAL fails to find its DLLs due to
+      an interfering GDAL installation on the PATH, such as from anaconda.
+      https://github.com/natcap/invest/issues/1643
+    * Improved error handling of NA values in raster reclassification to provide
+      a more descriptive message.
 * Workbench
     * Several small updates to the model input form UI to improve usability
       and visual consistency (https://github.com/natcap/invest/issues/912).
@@ -64,14 +69,41 @@ Unreleased Changes
       (https://github.com/natcap/invest/issues/1609).
     * Improved error handling when a datastack cannot be saved with relative
       paths across drives (https://github.com/natcap/invest/issues/1608).
+    * The InVEST changelog now displays in the Workbench the first time a new
+      version is launched (https://github.com/natcap/invest/issues/1368).
+* Coastal Vulnerability
+    * Fixed a regression where an AOI with multiple features could raise a
+      TypeError after intersecting with the landmass polygon.
+      https://github.com/natcap/invest/issues/1657
+* Forest Carbon Edge Effects
+    * Updating vector reprojection to allow partial reprojection.  Related to
+      https://github.com/natcap/invest/issues/1645
 * Habitat Quality
     * Access raster is now generated from the reprojected access vector
       (https://github.com/natcap/invest/issues/1615).
     * Rarity values are now output in CSV format (as well as in raster format)
       (https://github.com/natcap/invest/issues/721).
+    * Improved error handling when there is a missing LULC value in the
+      sensitivity table (https://github.com/natcap/invest/issues/1671).
+* Pollination
+    * Fixed an issue with nodata handling that was causing some outputs to be
+      filled either with the float32 value for positive infinity, or else with
+      a value very close to it. https://github.com/natcap/invest/issues/1635
+    * While working on https://github.com/natcap/invest/issues/1635, we also
+      updated the stated dtype of most pollination model outputs to be float32
+      instead of the float64 dtype that was being assumed previously.  This
+      will result in smaller output filesizes with minimal loss of precision.
+* Seasonal Water Yield
+    * Added support for zero padding in month numbers in ET and precipitation
+      file names (i.e., users can now name their file Precip_01.tif).
+      (https://github.com/natcap/invest/issues/1166)
 * Urban Flood Risk
     * Fields present on the input AOI vector are now retained in the output.
       (https://github.com/natcap/invest/issues/1600)
+* Urban Nature Access
+    * The model now works as expected when the user provides an LULC raster
+      that does not have a nodata value defined.
+      https://github.com/natcap/invest/issues/1293
 
 3.14.2 (2024-05-29)
 -------------------

Makefile

@@ -2,15 +2,15 @@
 DATA_DIR := data
 GIT_SAMPLE_DATA_REPO        := https://bitbucket.org/natcap/invest-sample-data.git
 GIT_SAMPLE_DATA_REPO_PATH   := $(DATA_DIR)/invest-sample-data
-GIT_SAMPLE_DATA_REPO_REV    := ab8c74a62a93fd0019de2bca064abc0a5a07afab
+GIT_SAMPLE_DATA_REPO_REV    := 0f8b41557753dad3670ba8220f41650b51435a93
 
 GIT_TEST_DATA_REPO          := https://bitbucket.org/natcap/invest-test-data.git
 GIT_TEST_DATA_REPO_PATH     := $(DATA_DIR)/invest-test-data
 GIT_TEST_DATA_REPO_REV      := 324abde73e1d770ad75921466ecafd1ec6297752
 
 GIT_UG_REPO                 := https://github.com/natcap/invest.users-guide
 GIT_UG_REPO_PATH            := doc/users-guide
-GIT_UG_REPO_REV             := f203ec069f9f03560c9a85b268e67ebb6b994953
+GIT_UG_REPO_REV             := 5ee3616d4549baf3b1e44e0fcef485145389e29a
 
 ENV = "./env"
 ifeq ($(OS),Windows_NT)
@@ -66,13 +66,16 @@ PYTHON_ARCH := $(shell $(PYTHON) -c "import sys; print('x86' if sys.maxsize <= 2
 
 GSUTIL := gsutil
 SIGNTOOL := SignTool
+RST2HTML5 := rst2html5
 
 # local directory names
 DIST_DIR := dist
 DIST_DATA_DIR := $(DIST_DIR)/data
 BUILD_DIR := build
 WORKBENCH := workbench
 WORKBENCH_DIST_DIR := $(WORKBENCH)/dist
+CHANGELOG_SRC := HISTORY.rst
+CHANGELOG_DEST := $(WORKBENCH)/changelog.html
 
 # The fork name and user here are derived from the git path on github.
 # The fork name will need to be set manually (e.g. make FORKNAME=natcap/invest)
@@ -141,6 +144,7 @@ help:
 	@echo "  binaries          to build pyinstaller binaries"
 	@echo "  apidocs           to build HTML API documentation"
 	@echo "  userguide         to build HTML version of the users guide"
+	@echo "  changelog         to build HTML version of the changelog"
 	@echo "  python_packages   to build natcap.invest wheel and source distributions"
 	@echo "  codesign_mac      to sign the mac disk image using the codesign utility"
 	@echo "  codesign_windows  to sign the windows installer using the SignTool utility"
@@ -366,6 +370,9 @@ deploy:
 	@echo "Application binaries (if they were created) can be downloaded from:"
 	@echo "  * $(DOWNLOAD_DIR_URL)"
 
+changelog:
+	$(RST2HTML5) $(CHANGELOG_SRC) $(CHANGELOG_DEST)
+
 # Notes on Makefile development
 #
 # * Use the -drR to show the decision tree (and none of the implicit rules)

README.rst

@@ -35,7 +35,6 @@ General Information
 Dependencies
 ------------
 
-Run ``make check`` to test if all required dependencies are installed on your system.
 OS-specific installation instructions are found either online at
 http://invest.readthedocs.io/en/latest/installing.html or locally at ``doc/api-docs/installing.rst``.
 
@@ -57,30 +56,50 @@ Or on Windows, use the following instead from a CMD prompt::
     > make env
     > .\env\bin\activate
 
-This makefile target is included for convenience ... you may of course choose to
-manage your own virtual environment.  ``requirements.txt``,
-``requirements-dev.txt`` and ``requirements-docs.txt`` list the python
-dependencies needed.
+This makefile target is included for convenience. It uses ``conda`` and installs packages from ``conda-forge``.
+It also uses the `-p` flag with `conda create`, creating a `./env` folder containing the environment.
 
-Using a different environment name
-""""""""""""""""""""""""""""""""""
-If you prefer a different name for your environment, you may pass the environment name as
+Using a different environment folder name
+"""""""""""""""""""""""""""""""""""""""""
+If you prefer a different path for your environment, you may pass the environment path as
 a parameter to make::
 
     $ make ENV=myEnv env
 
-You could then activate the environment created at ``myEnv``.
+You could then activate the environment created at ``./myEnv``.
 
 
 Using a different environment management tool
 """""""""""""""""""""""""""""""""""""""""""""
-The InVEST Makefile uses ``virtualenv`` to set up an environment, but this is
-not the only `environment management tool out there
-<https://packaging.python.org/tutorials/installing-packages/#creating-virtual-environments>`_.
-You may elect to manage your virtual environment a different way, independent
-of ``make env``.  The only requirement for the build process is that the required
-tools are available on your PATH and the required python packages can be imported.
+You may of course choose to manage your own virtual environment without using the Makefile.
+
+We suggest using ``conda`` or ``mamba`` and ``conda-forge``.
+
+``requirements.txt``, ``requirements-dev.txt`` and ``requirements-docs.txt`` list the python
+dependencies needed.
+
+Installing ``natcap.invest`` from local source code
+"""""""""""""""""""""""""""""""""""""""""""""""""""
+From an activated virtual environment, it's safest to uninstall any existing installation
+and then install `natcap.invest`::
+
+    $ pip uninstall natcap.invest
+    $ make install
+
+In practice, it can be convenient to use an "editable install" instead to avoid needing
+to uninstall & re-install after making changes to source code::
+
+   $ pip install -e .
+
+Note that with an editable install any changes to non-Python (Cython, C++) files will
+require compilation using one of the above installation methods.
+
+*The Workbench is not part of the* ``natcap.invest`` *Python package. See*
+``workbench/readme.md`` *for developer details.*
 
+A successful ``natcap.invest`` installation will include the InVEST CLI::
+
+    $ invest list
 
 Building InVEST Distributions
 -----------------------------
@@ -145,6 +164,13 @@ To build the user's guide::
 This will build HTML and PDF documentation, writing them to ``dist/userguide``
 and ``dist/InVEST_*_Documentation.pdf``, respectively.
 
+The User's Guide is maintained in a separate git repository. InVEST will build
+the User's Guide with the commit defined in the ``Makefile``::
+
+   GIT_UG_REPO                 := https://github.com/natcap/invest.users-guide
+   GIT_UG_REPO_PATH            := doc/users-guide
+   GIT_UG_REPO_REV             := f203ec069f9f03560c9a85b268e67ebb6b994953
+
 
 API Documentation
 +++++++++++++++++
@@ -168,22 +194,12 @@ build zip archives of the sample data::
 
 This will write the data zipfiles to ``dist/data``. ``git`` command is needed.
 
-Single archive of sample data
-+++++++++++++++++++++++++++++
-
-For trainings, it is especially convenient to distribute all sample data as a
-single zip archive.  As an added bonus, this single zip archive can be provided
-to the InVEST installer for Windows as either the 'Advanced' input on the front
-page of the installer, or by a CLI flag, thus preventing the installer from
-downloading datasets from the internet.  See
-``installer/windows/invest_installer.nsi`` for more details.  To build a single
-archive of all InVEST sample data::
-
-    $ make sampledata_single
-
-This will write the single sampledata archive to
-``dist/InVEST_*_sample_data.zip``.
+Sample data is tracked in a ``git-lfs`` repo and will be packaged based on the commit
+defined in the ``Makefile``::
 
+   GIT_SAMPLE_DATA_REPO        := https://bitbucket.org/natcap/invest-sample-data.git
+   GIT_SAMPLE_DATA_REPO_PATH   := $(DATA_DIR)/invest-sample-data
+   GIT_SAMPLE_DATA_REPO_REV    := 0f8b41557753dad3670ba8220f41650b51435a93
 
 Tests
 -----
@@ -197,6 +213,16 @@ To run tests on the suite of Ecosystem Service models in InVEST::
 
     $ make test
 
+Tests depend on test data that is tracked in a ``git-lfs`` repo defined in the ``Makefile``::
+
+   GIT_TEST_DATA_REPO          := https://bitbucket.org/natcap/invest-test-data.git
+   GIT_TEST_DATA_REPO_PATH     := $(DATA_DIR)/invest-test-data
+   GIT_TEST_DATA_REPO_REV      := 324abde73e1d770ad75921466ecafd1ec6297752
+
+Test data (and Sample Data) can be retrieved using::
+
+   $ make fetch
+
 
 Changing how GNU make runs tests
 ++++++++++++++++++++++++++++++++

doc/api-docs/conf.py

@@ -187,7 +187,7 @@
     natcap.invest.carbon.execute(args)
 
 For examples of scripting a model run, or multiple successive model runs,
-see :ref:`CreatingSamplePythonScripts`.
+see :ref:`CreatingPythonScripts`.
 
 
 .. contents:: Available Models and Tools: