Merge branch 'main' of https://github.com/NCAR/geocat-comp into custo…

…m_season_climatology

.github/PULL_REQUEST_TEMPLATE.md

@@ -18,7 +18,7 @@ apply to this PR, comment it out or delete it. -->
 
 **Functionality**
 - [ ] Function is in appropriate module file
-- [ ] New function(s) intended for public API added to `src/geocat/comp/__init__.py` file
+- [ ] New function(s) intended for public API added to `geocat/comp/__init__.py` file
 
 **Testing**
 - [ ] Tests for function exists in associated module test file

.github/workflows/ci-release.yml

@@ -16,7 +16,7 @@ jobs:
       fail-fast: false
       matrix:
         os: [ "ubuntu-latest", "macos-latest"]
-        python-version: [ "3.8", "3.9", "3.10" ]
+        python-version: ["3.9", "3.10", "3.11"]
     steps:
       - name: Cancel previous runs
         uses: styfle/cancel-workflow-action@0.11.0

.github/workflows/ci.yml

@@ -22,7 +22,7 @@ jobs:
       fail-fast: false
       matrix:
         os: [ "ubuntu-latest", "macos-latest"]
-        python-version: [ "3.8", "3.9", "3.10" ]
+        python-version: ["3.9", "3.10", "3.11"]
     steps:
       - name: Cancel previous runs
         uses: styfle/cancel-workflow-action@0.11.0
@@ -55,7 +55,7 @@ jobs:
 
       - name: Run Coverage Tests
         run: |
-          python -m pytest test -v --cov=./src/geocat/comp --cov-report=xml
+          python -m pytest test -v --cov=./geocat/comp --cov-report=xml
 
       - name: Upload code coverage to Codecov
         uses: codecov/codecov-action@v3.1.4

.github/workflows/upstream-dev-ci.yml

@@ -55,4 +55,4 @@ jobs:
 
       - name: Running Tests
         run: |
-          python -m pytest test -v --cov=./src/geocat/comp --cov-report=xml
+          python -m pytest test -v --cov=./geocat/comp --cov-report=xml

.gitignore

@@ -1,7 +1,7 @@
 /build/
 
 # Dask
-/src/geocat/comp/dask-worker-space/
+geocat/comp/dask-worker-space/
 
 
 # Created by https://www.gitignore.io/api/python,intellij,intellij+all,intellij+iml

.pre-commit-config.yaml

@@ -1,6 +1,6 @@
 repos:
--   repo: https://github.com/pre-commit/mirrors-yapf    # To format the code to conform YAPF
-    rev: v0.31.0
+-   repo: https://github.com/google/yapf    # To format the code to conform YAPF
+    rev: v0.33.0
     hooks:
       - id: yapf
         args: ['--in-place', '--recursive', '--style', 'google']

.readthedocs.yml

@@ -11,7 +11,6 @@ build:
     python: "mambaforge-4.10"
   jobs:
     post_create_environment:
-      - pip install geocat-f2py
       - python -m pip install --no-cache-dir .
 
 # Build documentation in the docs/ directory with Sphinx

CONTRIBUTING.md

@@ -6,19 +6,19 @@ following contribution guidelines:
 # Adding new functions to the Geocat-comp repo
 
 1. For a new function or family of functions that handle similar computations, create a new Python file in
-`$GEOCATCOMP/src/geocat/comp/`.
+`$GEOCATCOMP/geocat/comp/`.
 
 2. For implementation guidelines (such as Xarray and Dask usage), please refer to:
    - Previously implemented functionality as examples,
-    e.g. [polynomial.py](https://github.com/NCAR/geocat-comp/blob/main/src/geocat/comp/polynomial.py) or others.
+    e.g. [polynomial.py](https://github.com/NCAR/geocat-comp/blob/main/geocat/comp/polynomial.py) or others.
    - [GeoCAT Contributor's Guide](https://geocat.ucar.edu/pages/contributing.html) for further information.
 
-3. In any Python script under `$GEOCATCOMP/src/geocat/comp/`, there may be user API functions, which are
+3. In any Python script under `$GEOCATCOMP/geocat/comp/`, there may be user API functions, which are
 supposed to be included in the `geocat.comp` namespace, and internal API functions, which are used by the
 user API functions as helpers, preferably starts with an underscore ("_") in their names, as well as are
 not included in the `geocat.comp` namespace.
 
-4. The user API functions should be imported in `$GEOCATCOMP/src/geocat/comp/__init__.py` to be included in
+4. The user API functions should be imported in `$GEOCATCOMP/geocat/comp/__init__.py` to be included in
 the namespace.
 
 5. For appropriate documentation, each user API and internal API function should be listed in the

MANIFEST.in

@@ -1,7 +1,7 @@
 include LICENSE
 include README.md
 
-recursive-include src *.py
+recursive-include geocat *.py
 recursive-exclude * __pycache__
 recursive-exclude * *.py[co]
 

README.md

@@ -13,27 +13,6 @@ project and a single Github repository as described here. As the computational c
 on geosciences data. Many of these functions originated in NCL and were translated into Python with the help of GeoCAT-comp;
 however, developers are welcome to come up with novel computational functions for geosciences data.
 
-Many of the computational functions in GeoCAT are implemented in a pure Python fashion. However,
-there are some others that are implemented in Fortran but wrapped up in Python. To facilitate
-contribution, the whole GeoCAT-comp structure is split into two repositories with respect to
-being pure-Python or Python with compiled codes (i.e. Fortran) implementations. Such implementation
-layers are handled within [GeoCAT-comp](https://github.com/NCAR/geocat-comp) and
-[GeoCAT-f2py](https://github.com/NCAR/geocat-f2py) repositories, respectively (The
-[GeoCAT-f2py](https://github.com/NCAR/geocat-f2py) repo is documented on its own).
-
-
-# GeoCAT-comp
-
-GeoCAT-comp repo does not explicitly contain or require any compiled code, making it more
-accessible to the general Python community at large. However, if
-[GeoCAT-f2py](https://github.com/NCAR/geocat-f2py) is installed, then all functions contained in
-the "geocat.f2py" package are imported seamlessly into the "geocat.comp" namespace. Thus,
-GeoCAT-comp repo serves as a user API to access the entire computational toolkit even though the
-repo itself only contains pure Python code from the contributor’s perspective. Whenever prospective
-contributors want to add new computational functionality implemented as pure Python, GeoCAT-comp
-is the repo to do so. Therefore, there is no onus on contributors of pure python code to
-build/compile/test any compiled code (i.e. Fortran) at GeoCAT-comp level.
-
 
 # Documentation
 
@@ -50,15 +29,6 @@ Please see our documentation for
 [installation and build instructions](https://github.com/NCAR/geocat-comp/blob/main/INSTALLATION.md).
 
 
-# Xarray interface vs NumPy interface
-
-GeoCAT-comp provides a high-level [Xarray](http://xarray.pydata.org/en/stable/) interface under the
-`geocat.comp` namespace. However, a stripped-down NumPy interface is used under the hood to bridge
-the gap between NumPy arrays and the compiled language data structures used by
-[GeoCAT-f2py](https://github.com/NCAR/geocat-f2py). These functions are accessible under the
-`geocat.comp` namespace, but are minimally documented and are
-intended primarily for internal use.
-
 # Citing GeoCAT-comp
 
 If you use this software, please cite it as described at the [GeoCAT-comp - Citation](

build_envs/docs.yml

@@ -2,9 +2,8 @@ name: gc-docs
 channels:
     - conda-forge
 dependencies:
-    - python>=3.8, <3.11
+    - python>=3.9, <3.12
     - pre_commit
-    - geocat-f2py
     - geocat-datafiles
     - geocat-viz
     - xarray<=2023.02.0 #pin per issue #381

build_envs/environment.yml

@@ -2,13 +2,12 @@ name: geocat_comp_build
 channels:
   - conda-forge
 dependencies:
-  - python>=3.8, <3.11  # minimum support 3.8, 3.11 not yet fully supported
+  - python>=3.9, <3.12  # minimum support 3.9
   - cf_xarray>=0.3.1    # min version 0.3.1 for dependencies
   - cftime
   - dask
   - distributed
   - eofs
-  - geocat-f2py
   - metpy
   - numba
   - numpy<1.24  # 1.24 not yet fully compatible with numba

build_envs/upstream-dev-environment.yml

@@ -2,11 +2,10 @@ name: geocat_comp_upstream
 channels:
   - conda-forge
 dependencies:
-  - python>=3.8, <3.11
+  - python>=3.9
   - cftime
   - eofs
   - geocat-datafiles  # for tests
-  - geocat-f2py
   - netcdf4  # for tests
   - parameterized  # for tests
   - pytest  # for tests

docs/getting_started/overview.rst

@@ -41,7 +41,5 @@ GeoCAT-f2py
 -----------
 While our goal is to recreate NCL functions in pure Python, translating some NCL routines is challenging and time
 consuming. To ensure GeoCAT users have access to those functions while we work on full Python versions, the Fortran code
-they are based upon is wrapped in Python in the GeoCAT-f2py (Fortran 2 Python) package. GeoCAT-f2py is imported by
-GeoCAT-comp and included in the GeoCAT-comp namespace. Simply, this means that GeoCAT-f2py functions can be called
-through GeoCAT-comp, so there is no need for users to import GeoCAT-f2py directly in their scripts. Information about
+they are based upon is wrapped in Python in the GeoCAT-f2py package. Information about
 GeoCAT-f2py can be found on the `package's homepage <https://geocat-f2py.readthedocs.io/>`__.

docs/installation.rst

@@ -108,9 +108,6 @@ the dependencies for building and testing GeoCAT-comp.
 .. include:: ../build_envs/environment.yml
     :literal:
 
-Note: `GeoCAT-f2py <https://github.com/NCAR/geocat-f2py>`__ dependency will automatically
-install further dependencies for compiled language implementation.
-
 
 How to create a Conda environment for building GeoCAT-comp
 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^

docs/internal_api/index.rst

@@ -19,14 +19,10 @@ Internal Functionality Helpers
 
    geocat.comp.climatologies._calculate_center_of_time_bounds
 
-   geocat.comp.climatologies._find_time_invariant_vars
-
    geocat.comp.climatologies._get_time_coordinate_info
 
    geocat.comp.climatologies._infer_calendar_name
 
-   geocat.comp.climatologies._setup_clim_anom_input
-
    geocat.comp.climatologies._validate_freq
 
    geocat.comp.gradient._arc_lat_wgs84

docs/release-notes.rst

@@ -1,10 +1,11 @@
 .. currentmodule:: geocat.comp
 
 .. _release:
+
 Release Notes
 =============
 
-v2023.06.0 (Jun X, 2023)
+v2023.07.0 (Jul X, 2023)
 -----------------------
 [Plain text summary here]
 
@@ -14,6 +15,42 @@ New Features
 
 
 v2023.05.0 (May 4, 2023)
+--------------------------
+This releases fixes the unintentional limitation of the 2023.06.0 release to python 3.11.0
+
+Bug Fixes
+^^^^^^^^^
+* Fix python version limit of 3.11.0 by `Anissa Zacharias`_ in (:pr:`431`)
+
+
+v2023.06.0 (June 23, 2023)
+--------------------------
+This release removes the geocat-f2py dependency. To use these functions, users
+will need to install the geocat-f2py package directly. Additionally, this
+release also drops support for python 3.8 and adds support for 3.11.
+
+Documentation
+^^^^^^^^^^^^^
+* New *Vertically Integrated Moisture Flux Convergence* (VIMFC) example by `Julia Kent`_ in (:pr:`388`)
+
+Internal Changes
+^^^^^^^^^^^^^^^^
+* Updates deprecated pre-commit YAPF repository from https://github.com/pre-commit/mirrors-yapf to https://github.com/google/yapf by `Anissa Zacharias`_ in (:pr:`417`)
+* Reconfigures package structure to remove top level ``src/`` directory by `Anissa Zacharias`_ in (:pr:`419`)
+
+Breaking Changes
+^^^^^^^^^^^^^^^^
+* Removed deprecated functions ``climatology`` and ``anomaly`` by `Anissa Zacharias`_ in (:pr:`416`)
+* Removed internal functions ``_find_time_invariant_vars`` and ``_setup_clim_anom_input`` by `Anissa Zacharias`_ in (:pr:`416`)
+* Dropped support for python 3.8 (and added support for python 3.11) by `Anissa Zacharias`_ in (:pr:`426`)
+* Removed ``geocat-f2py`` dependency by `Anissa Zacharias`_ in (:pr:`421`)
+
+Bug Fixes
+^^^^^^^^^
+* Fix bug in `_temp_extrapolate` used by `interp_hybrid_to_pressure` by `Katelyn FitzGerald`_ in (:pr:`422`)
+
+
+v2023.05.0 (4 May 2023)
 -----------------------
 In this release, we've added support for numpy input and other improvements to the gradient function
 
@@ -75,6 +112,7 @@ Deprecations
 ^^^^^^^^^^^^
 * Remove deprecated functions from v2022.10.0 by `Heather Craker`_ in (:pr:`357`)
 * Remove links to deleted function docs by `Heather Craker`_ in (:pr:`359`)
+
 Bug Fixes
 ^^^^^^^^^
 * Partial fix for _vertical_remap_extrap bug by `Heather Craker`_ in (:pr:`360`)
@@ -193,3 +231,4 @@ Maintenance
 .. _`Alea Kootz`: https://github.com/pilotchute
 .. _`Mario Rodriguez`: https://github.com/marodrig
 .. _`Julia Kent`: https://github.com/jukent
+.. _`Katelyn FitzGerald`: https://github.com/kafitzgerald

docs/user_api/index.rst

@@ -91,24 +91,6 @@ Statistics
    eofunc_pcs
    pearson_r
 
-
-GeoCAT-comp routines from GeoCAT-f2py
--------------------------------------
-.. currentmodule:: geocat.comp
-.. autosummary::
-   :nosignatures:
-   :toctree: ./generated/
-
-   grid_to_triple
-   linint1
-   linint2
-   linint2pts
-   moc_globe_atl
-   rcm2points
-   rcm2rgrid
-   rgrid2rcm
-   triple_to_grid
-
 NCL Function Name Wrappers
 --------------------------
 .. currentmodule:: geocat.comp
@@ -118,15 +100,19 @@ NCL Function Name Wrappers
 
    meteorology.dpres_plev
 
-
 Deprecated Functions
---------------------
-Climatologies
-^^^^^^^^^^^^^
-.. currentmodule:: geocat.comp.climatologies
+---------------------
+.. currentmodule:: geocat.comp.deprecated
 .. autosummary::
    :nosignatures:
    :toctree: ./generated/
 
-   anomaly
-   climatology
+   grid_to_triple
+   linint1
+   linint2
+   linint2pts
+   moc_globe_atl
+   rcm2points
+   rcm2rgrid
+   rgrid2rcm
+   triple_to_grid

geocat/comp/__init__.py

@@ -0,0 +1,57 @@
+# move functions into geocat.comp namespace
+from .climatologies import (
+    month_to_season,
+    calendar_average,
+    climatology_average,
+    climate_anomaly,
+)
+from .fourier_filters import (
+    fourier_band_block,
+    fourier_band_pass,
+    fourier_filter,
+    fourier_high_pass,
+    fourier_low_pass,
+)
+from .gradient import gradient, _arc_lon_wgs84, _arc_lat_wgs84, _rad_lat_wgs84
+from .interpolation import (
+    interp_hybrid_to_pressure,
+    interp_sigma_to_hybrid,
+    interp_multidim,
+)
+from .meteorology import (
+    dewtemp,
+    heat_index,
+    relhum,
+    relhum_ice,
+    relhum_water,
+    actual_saturation_vapor_pressure,
+    max_daylight,
+    psychrometric_constant,
+    saturation_vapor_pressure,
+    saturation_vapor_pressure_slope,
+    delta_pressure,
+    dpres_plev,
+)
+from .spherical import decomposition, recomposition, scale_voronoi
+from .stats import eofunc, eofunc_eofs, eofunc_pcs, eofunc_ts, pearson_r
+from .deprecated import (
+    grid_to_triple,
+    linint1,
+    linint2,
+    linint2pts,
+    moc_globe_atl,
+    rcm2points,
+    rcm2rgrid,
+    rgrid2rcm,
+    triple_to_grid,
+)
+
+# get version from pyproject.toml
+from importlib.metadata import version as _version
+
+try:
+    __version__ = _version("geocat.comp")
+except Exception:
+    # Local copy or not installed with setuptools.
+    # Disable minimum version checks on downstream libraries.
+    __version__ = "999"