- changed test scripts to remove fixtures and start parameterizing using pytest-cases plugin

- updated management of `TEST_DATA` variable and moved its descendents to conftest.py
- updated location of images dir to docs dir
- deprecated modules `agreement_map.py`, `test_integration.py`, and `tests/utils.py`
- updated `spatial_alignment.py` to allow for `xr.Datasets` (not currently reflected in tests)
- deprecate `check_for_single_band_raster()`
- added test module for `load_raster_as_xarray()`
- updated docstring for `_is_not_natural_number()`
- converting input arg for `_is_not_natural_number(x)` to int to control for overflowerror
- converted `matching_spatial_indices()` to use `xr.align(*args,join='exact')`
- updated `transform_bounds()` to remove dst_crs arg
- renamed target_map to _crs on `transform_bounds()`
- made changes to `_check_file()` to avoid reopening S3 client and moved s3 name to module variable
- added `_build_map_file_path()` to help build filepaths for test data
- moved case with xarray objects up in if/else block within `align_rasters`
- general housekeeping

Author: fernando-aristizabal

README.MD

@@ -7,7 +7,7 @@ maps and metrics.
 NOTE: THIS PACKAGE IS UNDER ACTIVE DEVELOPMENT AND NOT CURRENTLY
 FUNCTIONING. BREAKING CHANGES ARE OFTEN INTRODUCED.
 
-![alt text](./images/ExampleWorkflow.png)
+![alt text](../../docs/images/ExampleWorkflow.png)
 
 # Installation
 
@@ -21,18 +21,18 @@ To use this package:
 
 ## Standards
 
-  - Python 3.10 or higher
-  - [Numpy Style Docstrings](https://numpydoc.readthedocs.io/en/v1.1.0/format.html#documenting-modules)
-  - [Python Type Hints](https://docs.python.org/3/library/typing.html)
-  - [PEP8](https://pep8.org/) Styling (and
-    [this](https://peps.python.org/pep-0008/))
+- Python 3.10 or higher
+- [Numpy Style Docstrings](https://numpydoc.readthedocs.io/en/v1.1.0/format.html#documenting-modules)
+- [Python Type Hints](https://docs.python.org/3/library/typing.html)
+- [PEP8](https://pep8.org/) Styling (and
+  [this](https://peps.python.org/pep-0008/))
 
 ## Code Dependencies
 
-  - [rioxarray](https://corteva.github.io/rioxarray/html/index.html)
-  - [geopandas](https://geopandas.org/en/stable/)
-  - [dask](https://www.dask.org)
-  - [xarray-spatial](https://xarray-spatial.org)
+- [rioxarray](https://corteva.github.io/rioxarray/html/index.html)
+- [geopandas](https://geopandas.org/en/stable/)
+- [dask](https://www.dask.org)
+- [xarray-spatial](https://xarray-spatial.org)
 
 # Contributing
 
@@ -44,8 +44,8 @@ To use this package:
 
 There are two primary ways to help:
 
-  - Using the issue tracker, and
-  - Changing the code-base.
+- Using the issue tracker, and
+- Changing the code-base.
 
 ## Using the issue tracker
 
@@ -67,7 +67,7 @@ stylistic and architectural guidelines prescribed by the project. In the
 absence of such guidelines, mimic the styles and patterns in the
 existing code-base.
 
-![alt text](./images/ContributionGraphic.png)
+![alt text](../../docs/images/ContributionGraphic.png)
 
 ### Guidelines
 
@@ -87,34 +87,33 @@ If you would like to contribute, please follow the following steps:
 
 ## Tooling Dependencies
 
-  - Code Checking with [Flake8](https://github.com/PyCQA/flake8)
-      - Combines PyFlakes, pycodestyle, and others for linting and style
-        checking.
-      - For autoformatting:
-        [flake8-black](https://pypi.org/project/flake8-black/)
-  - Testing with
-    [PyTest](https://docs.pytest.org/en/7.1.x/contents.html)
-      - For timed tests:
-        [pytest-benchmark](https://pypi.org/project/pytest-benchmark/)
-      - For code coverage:
-        [pytest-cov](https://pypi.org/project/pytest-cov/)
-  - Profiling
-      - [yappi](https://github.com/sumerc/yappi/)
-      - For memory profiling: [memray](https://pypi.org/project/memray/)
-      - Dask memory profiling:
-        [dask-memusage](https://github.com/itamarst/dask-memusage)
-  - Dependencies and Packaging
-      - [pip](https://packaging.python.org/en/latest/key_projects/#pip)
-      - Docker
-  - Distribution
-      - [PyPI](https://pypi.org/)
-      - DockerHub
-      - GitHub (source, packaging, and images)
-  - Docs
-      - [Sphinx](https://www.sphinx-doc.org/)
-      - [pandoc](https://pypi.org/project/pandoc/)
-      - [ReadTheDocs](https://readthedocs.org/)
-      - [Jupyter](https://pypi.org/project/jupyter/)
+- Code Checking with [Flake8](https://github.com/PyCQA/flake8)
+  - Combines PyFlakes, pycodestyle, and others for linting and style
+    checking.
+  - For autoformatting:
+    [flake8-black](https://pypi.org/project/flake8-black/)
+- Testing with [PyTest](https://docs.pytest.org/en/7.1.x/contents.html)
+  - For timed tests:
+    [pytest-benchmark](https://pypi.org/project/pytest-benchmark/)
+  - For code coverage:
+    [pytest-cov](https://pypi.org/project/pytest-cov/)
+- Profiling
+  - [yappi](https://github.com/sumerc/yappi/)
+  - For memory profiling: [memray](https://pypi.org/project/memray/)
+  - Dask memory profiling:
+    [dask-memusage](https://github.com/itamarst/dask-memusage)
+- Dependencies and Packaging
+  - [pip](https://packaging.python.org/en/latest/key_projects/#pip)
+  - Docker
+- Distribution
+  - [PyPI](https://pypi.org/)
+  - DockerHub
+  - GitHub (source, packaging, and images)
+- Docs
+  - [Sphinx](https://www.sphinx-doc.org/)
+  - [pandoc](https://pypi.org/project/pandoc/)
+  - [ReadTheDocs](https://readthedocs.org/)
+  - [Jupyter](https://pypi.org/project/jupyter/)
 
 ## Development Installation
 
@@ -125,68 +124,62 @@ choice.)
 
 First setup docker instance and in the root directory of the project:
 
-` [sudo] docker build -t gval-image --target development .  `
+`[sudo] docker build -t gval-image --target development . `
 
 The default user named 'user' with UID 1001 is created. To use the same
 user and permissions you currently have on your machine override with
 build arguments:
 
-`[sudo] docker build -t gval-image --build-arg UID=$(id -u) --target
-development .`
+`[sudo] docker build -t gval-image --build-arg UID=$(id -u) --target development .`
 
 Standard run examples from the command line (standard, or overriding
 user with root):
 
-  - `[sudo] docker run -v $(pwd):/home/user/gval --name gval-python
-    gval-image`
-  - `[sudo] docker run -v $(pwd):/home/user/gval --user root --name
-    gval-python gval-image`
+- `[sudo] docker run -v $(pwd):/home/user/gval --name gval-python gval-image`
+- `[sudo] docker run -v $(pwd):/home/user/gval --user root --name gval-python gval-image`
 
 If given access keys for retrieving test data you can mount the volume
 as such:
 
-`[sudo] docker run -v ~/.aws:/home/user/.aws -v $(pwd):/home/user/gval
---name gval-python gval-image`
+`[sudo] docker run -v ~/.aws:/home/user/.aws -v $(pwd):/home/user/gval --name gval-python gval-image`
 
 To keep your container running, try adding `tail -f /dev/null` as your
 command ensuring to detach with `-d`:
 
-  - `[sudo] docker run -d -v $(pwd):/home/user/gval --name gval-python
-    gval-image tail -f /dev/null`
+- `[sudo] docker run -d -v $(pwd):/home/user/gval --name gval-python gval-image tail -f /dev/null`
 
 You can also set up your IDE to run this docker image directly:
 
-  - [PyCharm](https://www.jetbrains.com/help/pycharm/using-docker-as-a-remote-interpreter.html#config-docker)
-  - [Visual Studio
-    Code](https://code.visualstudio.com/docs/containers/quickstart-python)
+- [PyCharm](https://www.jetbrains.com/help/pycharm/using-docker-as-a-remote-interpreter.html#config-docker)
+- [Visual Studio
+  Code](https://code.visualstudio.com/docs/containers/quickstart-python)
 
 If the container already exists you can start as follows:
 
 `[sudo] docker start gval-python`
 
-To enter the container interactively: `[sudo] docker exec gval-python
-bash`
+To enter the container interactively:
+`[sudo] docker exec gval-python bash`
 
 ## Packaging
 
 To build the gval package and install locally:
 
-  - In the root directory install the gVal package:
+- In the root directory install the gVal package:
 
-    `python -m build && pip install dist/*.whl --force-reinstall`
+  `python -m build && pip install dist/*.whl --force-reinstall`
 
-  - Or on Windows replacing version number with current version number:
+- Or on Windows replacing version number with current version number:
 
-    `py -m build` then get the name of the wheel in the dist directory,
-    e.g.:
+  `py -m build` then get the name of the wheel in the dist directory,
+  e.g.:
 
-    `pip install dist/gval-0.0.1-py3-none-any.whl --force-reinstall`
+  `pip install dist/gval-0.0.1-py3-none-any.whl --force-reinstall`
 
 The packaging process using docker container would look as follows (on
 linux):
 
-`sudo docker exec -v $(pwd):/home/user/ --user root python -m build &&
-pip install dist/*.whl --force-reinstall`
+`sudo docker exec -v $(pwd):/home/user/ --user root python -m build && pip install dist/*.whl --force-reinstall`
 
 # Citation
 

config.py

@@ -1,11 +1,16 @@
+"""
+Package-level configuration file.
+"""
+
+# __all__ = ['*']
+__author__ = "Fernando Aristizabal, Gregory Petrochenkov"
+
+
 import os
 
-# Get absolute path of file
-abs_path = os.path.dirname(os.path.abspath(__file__))
 
-TEST_DATA = os.path.join(abs_path, "data", "data")
-# TEST_DATA = os.path.join("s3://gval-test")
-# AWS_KEYS = os.path.join(abs_path, "data", "access_keys.csv")
+# defines absolute path of project's root directory
+PROJECT_DIR = os.path.dirname(os.path.abspath(__file__))
 
 
 if __name__ == "__main__":

images/ContributionGraphic.png renamed to docs/images/ContributionGraphic.png

@@ -3,4 +3,4 @@ gVal (pronounced "g-val") is a high-level Python framework to evaluate the geosp
 
 NOTE: THIS PACKAGE IS UNDER ACTIVE DEVELOPMENT AND NOT CURRENTLY FUNCTIONING. BREAKING CHANGES ARE OFTEN INTRODUCED.
 
-![alt text](../../images/ExampleWorkflow.png)
+![alt text](../../docs/images/ExampleWorkflow.png)

images/ExampleWorkflow.png renamed to docs/images/ExampleWorkflow.png

@@ -32,7 +32,7 @@ Additionally, the code should follow any stylistic and architectural guidelines
 prescribed by the project. In the absence of such guidelines, mimic the styles
 and patterns in the existing code-base.
 
-![alt text](../../images/ContributionGraphic.png)
+![alt text](../../docs/images/ContributionGraphic.png)
 
 ### Guidelines
 

docs/markdown/01_INTRO.MD

@@ -1,4 +1,3 @@
-from gval.outputs.agreement_map import Agreement_map
 from gval.homogenize.spatial_alignment import Spatial_alignment
 from gval.utils.exceptions import RasterMisalignment, RastersNotSingleBand
 from gval.utils.loading_datasets import load_raster_as_xarray

docs/markdown/05_CONTRIBUTING.MD

@@ -28,16 +28,30 @@ def _is_not_natural_number(x: Number) -> int:
     """
     Checks value to see if it is a natural number or two non-negative integer [0, 1, 2, 3, 4, ...)
 
-    FIXME: Must return boolean or some other numba type. Having trouble returning none.
+    Parameters
+    ----------
+    x : Number
+        Number to test.
+
+    Returns
+    -------
+    int
+        Return -2 by default. Issue with numba usage. Please ignore for now.
+        FIXME: Must return boolean or some other numba type. Having trouble returning none.
+
+    Raises
+    ------
+    ValueError
+        If x not a natural number.
     """
     # checks to make sure it's not a nan value
     if np.isnan(x):
         return -2  # dummy return
     # checks for non-negative and whole number
-    elif (x < 0) | ((x - int(x)) != 0):
+    elif (x < 0) | ((x - nb.int64(x)) != 0):
         # FIXME: how to print x with message below using numba????
         raise ValueError(
-            "Negative or non-whole number found (non-negative integers) [0, 1, 2, 3, 4, ...)"
+            "Non natural number found (non-negative integers, excluding Inf) [0, 1, 2, 3, 4, ...)"
         )
     # must return something according to signature
     else: