Merge pull request #314 from CosmiQ/dev

Version 0.2.0 release

.travis.yml

@@ -5,6 +5,7 @@ cache: false
 python:
   - "3.6"
   - "3.7"
+  - "3.8"
 
 # command to install dependencies
 install:
@@ -21,7 +22,7 @@ install:
   - hash -r
   - conda config --set always_yes yes --set changeps1 no
   # Useful for debugging any issues with conda
-  - conda install pip  # work around miniconda 4.7.12 bug
+  - conda install pip  # workaround to avoid miniconda 4.7.12 bugs
   - conda update conda -c conda-forge
   - conda info -a
   # switch python version spec in environment.yml to match TRAVIS_PYTHON_VERSION
@@ -32,11 +33,14 @@ install:
   - source activate solaris
   - python --version
   - pip install -q -e .[test]
-  - conda install pytest=4.6.2 -c conda-forge
-  - pip install codecov pytest-cov
+  - pip install codecov pytest-cov pytest==5.3.1
 # command to run tests
 script:
   - python -m pytest --cov=./
 
 after_success:
   - codecov
+
+jobs:
+    allow_failures:
+        - python: "3.8"

.vscode/settings.json

@@ -0,0 +1,9 @@
+{
+    "python.testing.pytestArgs": [
+        "tests"
+    ],
+    "python.testing.unittestEnabled": false,
+    "python.testing.nosetestsEnabled": false,
+    "python.testing.pytestEnabled": true,
+    "python.pythonPath": "/home/rave/miniconda3/envs/solaris-test/bin/python"
+}

CHANGELOG.md

@@ -4,11 +4,11 @@
 
 Anytime you add something new to this project, add a new item under the appropriate sub-heading of the [Unreleased](#unreleased) portion of this document. That item should be formatted as follows:
 ```
-[Date (ISO format)], [GitHub username]: [Short description of change] [(PR number)]
+- [Date (ISO format)], [GitHub username]: [Short description of change] [(PR number)]
 ```
 e.g.
 ```
-20190930, nrweir: Added changelog (#259)
+- 20190930, nrweir: Added changelog (#259)
 ```
 Consistent with the "one PR per task" paradigm, we recommend having only one changelog entry per PR whenever possible; however, multiple entries can be included for a single PR if needed to capture the full changeset.
 
@@ -17,18 +17,34 @@ When a new version of `solaris` is released, all of the changes in the Unrelease
 ## Unreleased
 
 ### Added
-20190930, nrweir: Added changelog
-
 ### Removed
-
 ### Changed
-
 ### Fixed
-
 ### Deprecated
-
 ### Security
 
+## Version 0.2.0
+
+### Added
+- 20190930, nrweir: Added CHANGELOG.md (#259)
+- 20190930, nrweir: Add contributing guidelines, CONTRIBUTING.md (#260)
+- 20191003, nrweir: Added `solaris.vector.mask.instance_mask()` (#261)
+- 20191009, nrweir: Added `solaris.data.coco` and some label utility functions (#265)
+- 20191009, nrweir: Added `solaris.data.coco` API documentation and a usage tutorial (#266)
+- 20191122, dphogan: Added option to take sigmoid of input in TorchDiceLoss (#281)
+- 20191122, dphogan: Inferer calls now take default DataFrame path from config dictionary (#282)
+- 20191125, nrweir: Added `solaris.utils.data.make_dataset_csv()` (#241)
+- 20191202, dphogan: Added fixed nodata value of 0 for mask files (#295)
+- 20191203: dphogan: Added filename argument to vector tiler's tile() (#297)
+- 20191211: rbavery: Tilers also accept rasterio CRS objects, `RasterTiler.tile` returns CRS object for vector tiler (#294)
+- 20191214: rbavery: tiler argument `aoi_bounds` is now `aoi_boundary` and can accept polygons besides boxes. functionaility for this moved to `solaris.utils.geo.split_geom` (#298)
+- 20191217: dphogan: Added support for custom loss functions (#308)
+
+### Fixed
+- 20191123, dphogan: Fixed issue in mask_to_poly_geojson() with empty GeoDataFrames.
+- 20191204, dphogan: Fixed issue with file output from footprint_mask() and contact_mask() (#301)
+- 20191212, jshermeyer: Fixed issue with vector tiling: could not load in list of sublists previously. Corrected comments for appropriate order as well. (#306)
+
 
 ---
 _The changelog for solaris was not implemented until after version 0.1.3, therefore no previous changes are recorded here. See the [GitHub releases](https://github.com/CosmiQ/solaris/releases) for available change records._

CONTRIBUTING.md

@@ -157,9 +157,13 @@ Every time Travis is triggered, it also calls on [Codecov](https://codecov.io) t
 ### Building docs
 
 Sphinx[http://www.sphinx-doc.org/en/stable/] is needed to build the documentation.
+You can install it and other necessary packages with conda.
+```
+conda install -c conda-forge sphinx sphinx_bootstrap_theme nbsphinx
+```
 
 To build docs, run ``make`` from the ``doc`` directory. ``make help`` lists
-all targets. For example, to build the HTML documentation, you can run `make html`. Then, all the HTML files will be generated in `solaris/docs/build/html`. To rebuild a full clean documentation, run:
+all targets. For example, to build the HTML documentation, you can run `make html`. Then, all the HTML files will be generated in `solaris/docs/_build/html`. To rebuild a full clean documentation, run:
 ```
 make clean
 make html

docs/api/data.rst

@@ -0,0 +1,12 @@
+.. title:: solaris.data API reference
+
+``solaris.data`` API reference
+===============================
+
+.. contents::
+
+``solaris.data.coco`` COCO label format management
+--------------------------------------------------
+
+.. automodule:: solaris.data.coco
+   :members:

docs/api/index.rst

@@ -14,7 +14,7 @@ Complete submodule documentation
 * `solaris.nets <nets.html>`_: Deep learning model ingestion, creation, training, and inference
 * `solaris.eval <eval.html>`_: Deep learning model performance evaluation
 * `solaris.utils <utils.html>`_: Utility functions for the above toolsets
-
+* `solaris.data <data.html>`_: Data management and format interconversion
 
 Submodule summaries
 ===================
@@ -28,6 +28,7 @@ Submodule summaries
    nets
    eval
    utils
+   data
 
 CLI commands
 ============

docs/conf.py

@@ -24,8 +24,8 @@
 copyright = u'2018-{}, CosmiQ Works: an IQT Lab'.format(time.strftime("%Y"))
 
 # The full version, including alpha/beta/rc tags
-release = '0.1.3'
-version = '0.1.3'
+release = '0.2.0'
+version = '0.2.0'
 
 # -- General configuration ---------------------------------------------------
 

docs/tutorials/index.rst

@@ -70,7 +70,7 @@ the tutorials below.
 * `Training a custom model <notebooks/api_training_custom.ipynb>`_
 * `Converting pixel masks to vector labels <notebooks/api_mask_to_vector.ipynb>`_
 * `Scoring your model's performance with the solaris Python API <notebooks/api_evaluation_tutorial.ipynb>`_
-
+* `Creating COCO-formatted datasets <notebooks/api_coco_tutorial.ipynb>`_
 
 Reference
 =========