BLD: Consolidate build configurations and rebuilt requirements (#27)

* BLD: Consolidated build configurations and rebuilt requirements

* Fixed pyproject vars and added atomicwrites dependency

* Fix build issues in test and added Dockerfile

* Added missing sympy dependency from broken laika package

.github/workflows/testing.yml

@@ -19,7 +19,7 @@ jobs:
         python-version: ${{ matrix.python-version }}
 
     - name: Install system-deps (for pycurl)
-      run: sudo apt-get install libcurl4-gnutls-dev libgnutls28-dev
+      run: sudo apt-get install -y libcurl4-openssl-dev libgeos-dev
     - name: Install Python packgaes
       run: |
         # These packages are installed in the base environment but may be older
@@ -33,4 +33,4 @@ jobs:
     - name: Test with pytest
       run: |
         coverage run -m pytest -vv
-        coverage report -m
+        coverage report -m

Dockerfile

@@ -0,0 +1,17 @@
+FROM python:3.9
+
+# Java needed for Spark API
+RUN apt-get update -y \
+    && apt-get install -y libcurl4-openssl-dev libgeos-dev
+
+WORKDIR /tmp
+
+COPY requirements-dev.txt .
+COPY tid tid/
+COPY .codecov.yml .
+COPY pyproject.toml .
+
+# Install python dependencies
+RUN pip install -r requirements-dev.txt
+
+ENTRYPOINT coverage run -m pytest -vv

README.md

@@ -3,7 +3,16 @@
 This library is designed to look for traveling ionospheric disturbances
 This branch is in a "being rewritten" state.
 
+## Setup
+Some platform-specific dependencies must be installed first:
+### Ubuntu (20.04)
+`sudo apt install gcc g++ libcurl4-dev libgeos-dev proj-bin`
+### MacOS
+`brew install proj`
 
+Following this, you should be able to install the requirements with
+
+`python -m pip install -r requirements.txt`
 
 ## Contributing
 Please ensure pylint and mypy are happy before pushing code.

pyproject.toml

@@ -1,3 +1,47 @@
+[build-system]
+requires = ["setuptools"]
+build-backend = "setuptools.build_meta"
+
+[project]
+name = "tid"
+version = "0.1.0"
+description = "Ionospheric measurements from GPS to detect launches."
+authors = [
+    {name = "Tyler Nighswander"},
+    {name = "Michael Nute"}
+]
+classifiers = [
+    "Development Status :: 2 - Pre-Alpha",
+    "Natural Language :: English",
+    "Programming Language :: Python :: 3",
+]
+license = {file = "LICENSE"}
+readme = "README.md"
+requires-python = ">=3.8"
+dependencies = [
+    "atomicwrites",
+    "awkward",
+    "cartopy",
+    "georinex",
+    "hatanaka",
+    "h5py",
+    "laika@git+https://github.com/commaai/laika#egg=laika",
+    "matplotlib",
+    "numpy",
+    "pyyaml",
+    "ruptures",
+    "scipy",
+    "sympy",
+    "xarray"
+]
+
+[project.urls]
+repository = "https://github.com/tylerni7/missile-tid"
+
+[tool.setuptools.packages.find]
+exclude = ["docs", "tests"]
+namespaces = false  # true by default
+
 [tool.mypy]
 python_version = "3.8"
 
@@ -23,12 +67,27 @@ ignore_missing_imports = true
 
 [tool.pylint.'MESSAGES CONTROL']
 max-line-length = 100
-max-attributes=12
-max-args=10
-max-locals=20
-min-public-methods=0
+max-attributes = 12
+max-args = 10
+max-locals = 20
+min-public-methods = 0
 # accepted short names: i,j,k for iteration
 # t for time
 # f1,f2 for frequencies
-good-names=['i,j,k,t,f1,f2']
-ignore=["tests"]
+good-names = ["i,j,k,t,f1,f2"]
+ignore = ["tests"]
+
+[tool.coverage.run]
+source = ["tid"]
+
+[tool.coverage.report]
+omit = [
+    "*/python?.?/*",
+    "*/site-packages/nose/*",
+    # ignore _version.py and versioneer.py
+    ".*version.*",
+    "*_version.py"
+]
+exclude_lines = [
+    "if __name__ == '__main__':"
+]

requirements-dev.txt

@@ -1,14 +1,59 @@
-# These are required for developing the package (running the tests, building
-# the documentation) but not necessarily required for _using_ it.
-codecov
-coverage
-flake8
-pytest
-sphinx
-twine
-# These are dependencies of various sphinx extensions for documentation.
-ipython
-matplotlib
-numpydoc
-sphinx-copybutton
-sphinx_rtd_theme
+atomicwrites==1.4.1
+attrs==22.2.0
+awkward==2.0.4
+awkward-cpp==5
+black==22.12.0
+Cartopy==0.21.1
+certifi==2022.12.7
+charset-normalizer==2.1.1
+click==8.1.3
+contourpy==1.0.6
+coverage==7.0.1
+cycler==0.11.0
+exceptiongroup==1.1.0
+flake8==6.0.0
+fonttools==4.38.0
+georinex==1.16.1
+h5py==3.7.0
+hatanaka==2.8.0
+idna==3.4
+importlib-resources==5.10.1
+iniconfig==1.1.1
+kiwisolver==1.4.4
+laika @ git+https://github.com/commaai/laika@5eb0c3c2596dd12a232b83bdb057a716810e89cf
+matplotlib==3.6.2
+mccabe==0.7.0
+mpmath==1.2.1
+mypy==0.991
+mypy-extensions==0.4.3
+ncompress==1.0.0
+numpy==1.24.1
+packaging==22.0
+pandas==1.5.2
+pathspec==0.10.3
+Pillow==9.3.0
+platformdirs==2.6.0
+pluggy==1.0.0
+pycodestyle==2.10.0
+pycurl==7.45.2
+pyflakes==3.0.1
+pyparsing==3.0.9
+pyproj==3.4.1
+pyshp==2.3.1
+pytest==7.2.0
+python-dateutil==2.8.2
+pytz==2022.7
+PyYAML==6.0
+requests==2.28.1
+scipy==1.9.3
+setuptools-scm==7.1.0
+Shapely==1.8.4
+six==1.16.0
+sympy==1.11.1
+tomli==2.0.1
+tqdm==4.64.1
+typing_extensions==4.4.0
+unlzw3==0.2.1
+urllib3==1.26.13
+xarray==2022.12.0
+zipp==3.11.0

requirements.txt

@@ -1,9 +1,43 @@
-# List required packages in this file, one per line.
-
-georinex
-h5py
-laika @ git+https://github.com/commaai/laika#egg=laika
-matplotlib
-numpy
-ruptures
-scipy
+atomicwrites==1.4.1
+awkward==2.0.4
+awkward-cpp==5
+Cartopy==0.21.1
+certifi==2022.12.7
+charset-normalizer==2.1.1
+contourpy==1.0.6
+cycler==0.11.0
+fonttools==4.38.0
+georinex==1.16.1
+h5py==3.7.0
+hatanaka==2.8.0
+idna==3.4
+importlib-resources==5.10.1
+kiwisolver==1.4.4
+laika @ git+https://github.com/commaai/laika@5eb0c3c2596dd12a232b83bdb057a716810e89cf
+matplotlib==3.6.2
+mpmath==1.2.1
+ncompress==1.0.0
+numpy==1.24.1
+packaging==22.0
+pandas==1.5.2
+Pillow==9.3.0
+pycurl==7.45.2
+pyparsing==3.0.9
+pyproj==3.4.1
+pyshp==2.3.1
+python-dateutil==2.8.2
+pytz==2022.7
+PyYAML==6.0
+requests==2.28.1
+scipy==1.9.3
+setuptools-scm==7.1.0
+Shapely==1.8.4
+six==1.16.0
+sympy==1.11.1
+tomli==2.0.1
+tqdm==4.64.1
+typing_extensions==4.4.0
+unlzw3==0.2.1
+urllib3==1.26.13
+xarray==2022.12.0
+zipp==3.11.0