Merge bde53eb into 5691803

.bandit

@@ -0,0 +1,3 @@
+[bandit]
+skips: B506
+exclude: uwsift/tests

.github/workflows/ci.yaml

@@ -17,7 +17,7 @@ jobs:
       - name: Set up Python
         uses: actions/setup-python@v2
         with:
-          python-version: 3.9
+          python-version: 3.11
       - name: Install dependencies
         run: |
           python -m pip install --upgrade pip
@@ -73,10 +73,10 @@ jobs:
         # XXX: We don't currently have OpenGL installation on other platforms
         #os: ["windows-latest", "ubuntu-latest", "macos-latest"]
         os: ["ubuntu-latest"]
-        python-version: ["3.7", "3.10"]
+        python-version: ["3.8", "3.10"]
         experimental: [false]
         include:
-          - python-version: "3.9"
+          - python-version: "3.10"
             os: "ubuntu-latest"
             experimental: true
 
@@ -159,4 +159,3 @@ jobs:
         uses: AndreMiras/coveralls-python-action@develop
         with:
           parallel-finished: true
-

.github/workflows/deploy.yaml

@@ -99,4 +99,4 @@ jobs:
       - uses: pypa/gh-action-pypi-publish@master
         with:
           user: __token__
-          password: ${{ secrets.UWSIFT_PYPI_TOKEN }}
+          password: ${{ secrets.UWSIFT_PYPI_TOKEN }}

.gitignore

@@ -109,3 +109,9 @@ venv.bak/
 
 # mypy
 .mypy_cache/
+
+# CMake build system
+CMakeCache.txt
+cmake_install.cmake
+CMakeFiles/
+Makefile

.pre-commit-config.yaml

@@ -1,19 +1,50 @@
 exclude: '^$'
 fail_fast: false
 repos:
-  #- repo: https://github.com/psf/black
-  #  rev: 20.8b1 # Replace by any tag/version: https://github.com/psf/black/tags
-  #  hooks:
-  #    - id: black
-  #      language_version: python3 # Should be a command that runs python3.6+
-  - repo: https://gitlab.com/pycqa/flake8
-    rev: 3.9.2
+  - repo: https://github.com/psf/black
+    rev: 22.3.0
+    hooks:
+      - id: black
+        language_version: python3
+        args:
+          - --target-version=py38
+  - repo: https://github.com/pycqa/isort
+    rev: 5.12.0
+    hooks:
+      - id: isort
+        language_version: python3
+  - repo: https://github.com/pycqa/flake8
+    rev: 4.0.1
     hooks:
       - id: flake8
         language_version: python3
-        additional_dependencies: [flake8-docstrings, flake8-debugger, flake8-bugbear]
-  #- repo: https://github.com/pycqa/isort
-  #  rev: 5.8.0
-  #  hooks:
-  #  - id: isort
-  #    language_version: python3
+        additional_dependencies: [flake8-docstrings, flake8-debugger, flake8-bugbear, mccabe]
+        args: [--max-complexity, "10"]
+  - repo: https://github.com/pre-commit/pre-commit-hooks
+    rev: v4.2.0
+    hooks:
+      - id: trailing-whitespace
+      - id: end-of-file-fixer
+      - id: check-yaml
+        args: [--unsafe]
+        # conda-recipes use jinja templating which isn't valid YAML syntax
+        exclude: conda-recipe\/
+  - repo: https://github.com/PyCQA/bandit
+    rev: '1.7.4'
+    hooks:
+      - id: bandit
+        args: [--ini, .bandit]
+  - repo: https://github.com/pre-commit/mirrors-mypy
+    rev: 'v0.991'  # Use the sha / tag you want to point at
+    hooks:
+      - id: mypy
+        additional_dependencies:
+          - types-docutils
+          - types-pkg-resources
+          - types-PyYAML
+          - types-requests
+          - types-python-dateutil
+ci:
+  # To trigger manually, comment on a pull request with "pre-commit.ci autofix"
+  autofix_prs: false
+  skip: [bandit, mypy]

AUTHORS.md

@@ -11,6 +11,12 @@ The following people have made contributions to this project:
 - [Jordan Gerth (jgerth)](https://github.com/jgerth)
 - [David Hoese (djhoese)](https://github.com/djhoese)
 - [Sauli Joro (sjoro)](https://github.com/sjoro)
+- [Nicolai Kellerer (nbke)](https://github.com/nbke)
+- [Max Kreischer (MaxKreischer)](https://github.com/MaxKreischer)
+- [Alexandra Melzer (armelzer)](https://github.com/armelzer)
+- [Andrea Meraner (ameraner)](https://github.com/ameraner)
 - [Coda Phillips (CodaP)](https://github.com/CodaP)
+- [Alexander Rettig (arcanerr)](https://github.com/arcanerr)
 - [William Roberts (wroberts4)](https://github.com/wroberts4)
 - [Eva Schiffer (evas-ssec)](https://github.com/evas-ssec)
+- [Johan Strandgren (strandgren)](https://github.com/strandgren)

CHANGELOG.md

@@ -271,4 +271,3 @@ In this release 1 pull request was closed.
 
 
 ## Version 1.0.0 (2018/10/25)
-

CMakeLists.txt

@@ -0,0 +1,157 @@
+#
+# Build System to create Conda and PyInstaller Packages for SIFT
+#
+#
+# Author: Alexander Rettig
+cmake_minimum_required( VERSION 3.10 ) # May be relaxed to allow older CMake versions but not below 3.8 because we use COMMAND_EXPAND_LISTS
+
+# 'LANGUAGES' might be changed to Python when a Python toolchain becomes available
+project( sift LANGUAGES NONE )
+
+#-------------------------------------------------------------------------------------------------
+# Global Settings
+#-------------------------------------------------------------------------------------------------
+
+list( APPEND CMAKE_MODULE_PATH "cmake/" )
+
+set( PYTHON_VERSION 3.10 CACHE STRING "Version of Python to setup/build SIFT for." )
+
+#-------------------------------------------------------------------------------------------------
+# Dependencies
+#-------------------------------------------------------------------------------------------------
+
+# Building packages is only supported from within a conda environment (for now)
+find_package( Conda REQUIRED )
+
+#-------------------------------------------------------------------------------------------------
+# Common Packaging Settings
+#-------------------------------------------------------------------------------------------------
+
+if( NOT ${PROJECT_NAME}_CONDA_ENVIRONMENT )
+  set( ${PROJECT_NAME}_CONDA_ENVIRONMENT "devel-${PYTHON_VERSION}" CACHE STRING "Name (or absolute path) of conda environment in which ${PROJECT_NAME} is build/packaged" )
+endif()
+
+if( "${${PROJECT_NAME}_CONDA_ENVIRONMENT}" STREQUAL "base" )
+  set( ${PROJECT_NAME}_CONDA_ENVIRONMENT "devel-${PYTHON_VERSION}" CACHE STRING "Name (or absolute path) of conda environment in which ${PROJECT_NAME} is build/packaged" FORCE )
+  message( FATAL_ERROR "${PROJECT_NAME} project must not be set up in a Conda 'base' environment. Resetting to sensible default." )
+endif()
+
+set( ${PROJECT_NAME}_DEPENDENCIES_CHANNEL "conda-forge" CACHE STRING "Conda channel which provides dependencies of ${PROJECT_NAME}." )
+
+#-------------------------------------------------------------------------------------------------
+# Convenience Target 'devel-bootstrap'
+#-------------------------------------------------------------------------------------------------
+
+# Support bootstrap a development environment
+# Prerequisite: Anaconda3 is installed, environment (base) activated
+
+if( ${Conda_EXECUTABLE} MATCHES .*/?mamba )
+  set( XRIT_DEFAULT ON )
+else()
+  set( XRIT_DEFAULT OFF )
+endif()
+option( WITH_xRITDecompress "If set, integrate xRITDecompress in the development environment" ${XRIT_DEFAULT} )
+
+add_custom_target( devel-bootstrap
+  COMMAND ${Conda_EXECUTABLE} create  --name ${${PROJECT_NAME}_CONDA_ENVIRONMENT} --channel conda-forge --strict-channel-priority python=${PYTHON_VERSION}
+  COMMAND ${Conda_EXECUTABLE} install --name ${${PROJECT_NAME}_CONDA_ENVIRONMENT} --channel conda-forge --strict-channel-priority --file conda-envs/sift-devel-minimal.pkgs
+
+  COMMAND ${CMAKE_COMMAND} -E $<IF:$<BOOL:${WITH_xRITDecompress}>,env,true> ${Conda_EXECUTABLE} install --name ${${PROJECT_NAME}_CONDA_ENVIRONMENT} --channel eumetsat --strict-channel-priority public-decomp-wt
+  COMMAND echo "You may want to run the following commands manually:"
+  COMMAND echo "  conda activate ${${PROJECT_NAME}_CONDA_ENVIRONMENT}"
+  COMMAND echo "  conda config --env --add channels conda-forge"
+  COMMAND echo "  conda config --env --set channel_priority strict"
+  COMMAND echo "  ${CMAKE_COMMAND} ."
+  COMMAND echo "To make sure that GRIB and BUFR readers work correctly, run the following commands manually:"
+  COMMAND echo "  pip install ecmwflibs"
+  COMMAND echo "  pip install eccodes"
+  COMMAND echo "  pip install cfgrib"
+  VERBATIM
+  COMMAND_EXPAND_LISTS
+  COMMENT "Setting up conda environment for development ..."
+  )
+
+#-------------------------------------------------------------------------------------------------
+# Check: make sure the current environment is the one the build system was set up in.
+#-------------------------------------------------------------------------------------------------
+
+if( NOT "${Conda_ENVIRONMENT}" STREQUAL "${${PROJECT_NAME}_CONDA_ENVIRONMENT}" )
+  message( WARNING
+    "Current Conda environment '${Conda_ENVIRONMENT}' doesn't match the configured build environment '${${PROJECT_NAME}_CONDA_ENVIRONMENT}'!\n"
+    "Please run\n"
+    "  ${CMAKE_MAKE_PROGRAM} devel-bootstrap\n"
+    "to set up an initial development environment '${${PROJECT_NAME}_CONDA_ENVIRONMENT}'\n"
+    "or if it already exists:\n"
+    "  conda activate ${${PROJECT_NAME}_CONDA_ENVIRONMENT}\n"
+    "in your working shell\n"
+    "or synchronize the value of ${PROJECT_NAME}_CONDA_ENVIRONMENT in the CMake configuration.\n"
+    )
+  return()
+endif()
+
+#-------------------------------------------------------------------------------------------------
+# Conda Packaging
+#-------------------------------------------------------------------------------------------------
+
+option( DIST_Conda "If set, a target for building installers with Conda is created" ON )
+if( DIST_Conda )
+
+set( ${PROJECT_NAME}_CONDA_RECIPE "${PROJECT_NAME}" ) # Name of the Conda recipe, i.e. the directory name to look for 'meta.yaml' in
+set( ${PROJECT_NAME}_CONDA_DIST_DIR "$ENV{HOME}/conda-channels/uwsift" CACHE STRING "Path to local conda packages directory." )
+
+add_custom_target( conda-packages
+  COMMAND ${Conda_EXECUTABLE} build -c ${${PROJECT_NAME}_DEPENDENCIES_CHANNEL} --python ${PYTHON_VERSION} --prefix-length 30 --output-folder "${${PROJECT_NAME}_CONDA_DIST_DIR}" "conda-recipe/${${PROJECT_NAME}_CONDA_RECIPE}"
+  VERBATIM
+  COMMENT "Building conda package for distribution to end users ..."
+  )
+
+endif( DIST_Conda )
+
+#-------------------------------------------------------------------------------------------------
+# PyInstaller Packaging
+#-------------------------------------------------------------------------------------------------
+
+option( DIST_PyInstaller "If set, a target for building installers with PyInstaller is created" ON )
+if( DIST_PyInstaller )
+
+  find_package( PyInstaller REQUIRED )
+  find_package( SelfPackers )
+  if( NOT SELF_PACKER_FOR_EXECUTABLE )
+    message( "PyInstaller packaging: Consider to install UPX (https://upx.github.io/) to get a smaller package." )
+  endif()
+
+#-------------------------------------------------------------------------
+
+set( ${PROJECT_NAME}_PYINSTALLER_BASE_DIR "${CMAKE_BINARY_DIR}/../pyinstaller" CACHE STRING
+  "Path to where PyInstaller shall put its artefacts.\n
+   CAUTION: The directory must be outside the source tree to avoid that PyInstaller artefacts interfere with Conda packaging.\n
+   WARNING: The directory is *owned* by the build system, it will be removed and recreated by the target 'pyinstaller-package'!" )
+  message( WARNING "Please consider carefully: "
+    " The directory configured as ${PROJECT_NAME}_PYINSTALLER_BASE_DIR='${${PROJECT_NAME}_PYINSTALLER_BASE_DIR}'"
+    " is *owned* by the build system, it will be removed and recreated by the target 'pyinstaller-package'!" )
+
+message( "Creating target 'pyinstaller-package'" )
+set( _pyi_dir_ ${${PROJECT_NAME}_PYINSTALLER_BASE_DIR} )
+add_custom_command(OUTPUT pyinstaller-build
+  COMMAND ${CMAKE_COMMAND} -E remove_directory "${_pyi_dir_}"
+  COMMAND pip install -e .
+  COMMAND ${PyInstaller_EXECUTABLE} --distpath "${_pyi_dir_}/package" --workpath "${_pyi_dir_}/work" --clean -y ${PROJECT_NAME}-pyinstaller-package.spec
+  COMMAND ${CMAKE_COMMAND} -E make_directory "${_pyi_dir_}/dist/${PROJECT_NAME}"
+  COMMAND ${CMAKE_COMMAND} -E make_directory "${_pyi_dir_}/dist/${PROJECT_NAME}/logs"
+  COMMAND ${CMAKE_COMMAND} -E rename "${_pyi_dir_}/package/${PROJECT_NAME}/resources/bin" "${_pyi_dir_}/dist/${PROJECT_NAME}/bin"
+  COMMAND ${CMAKE_COMMAND} -E rename "${_pyi_dir_}/package/${PROJECT_NAME}/etc"           "${_pyi_dir_}/dist/${PROJECT_NAME}/etc"
+  COMMAND ${CMAKE_COMMAND} -E rename "${_pyi_dir_}/package/${PROJECT_NAME}"               "${_pyi_dir_}/dist/${PROJECT_NAME}/lib"
+  BYPRODUCTS "${_pyi_dir_}/dist/${PROJECT_NAME}/lib/${PROJECT_NAME}"
+  VERBATIM
+  COMMENT "Building PyInstaller package in '${_pyi_dir_}/dist/${PROJECT_NAME}/lib'"
+  )
+add_custom_target( pyinstaller-package
+  COMMAND ${CMAKE_COMMAND} -E tar "cf" "${PROJECT_NAME}.zip" --format=zip "${PROJECT_NAME}"
+  DEPENDS pyinstaller-build
+  BYPRODUCTS "${_pyi_dir_}/dist/${PROJECT_NAME}.zip"
+  WORKING_DIRECTORY "${_pyi_dir_}/dist"
+  VERBATIM
+  COMMENT "Package PyInstaller output for SIFT"
+)
+
+endif( DIST_PyInstaller )

CONTRIBUTING.rst

@@ -2,4 +2,4 @@ How to Contribute
 =================
 
 Information on contributing to SIFT can be found on our
-[GitHub Wiki](https://github.com/ssec/sift/wiki/Contributing).
+[GitHub Wiki](https://github.com/ssec/sift/wiki/Contributing).

INSTALLER_README.md

@@ -61,7 +61,7 @@ Configuration files for the application are stored in the user's
 The downloaded tarball `.tar.gz` can be extracted by running:
 
     tar -xf SIFT_X.Y.Z.tar.gz
-    
+
 SIFT can then be started by running the `SIFT/SIFT` executable. Run
 `SIFT/SIFT -h` for available command line options.
 

LICENSE.txt

@@ -671,4 +671,4 @@ into proprietary programs.  If your program is a subroutine library, you
 may consider it more useful to permit linking proprietary applications with
 the library.  If this is what you want to do, use the GNU Lesser General
 Public License instead of this License.  But first, please read
-<https://www.gnu.org/licenses/why-not-lgpl.html>.
+<https://www.gnu.org/licenses/why-not-lgpl.html>.

README.md

@@ -5,6 +5,7 @@
 ![CI](https://github.com/ssec/sift/actions/workflows/ci.yaml/badge.svg)
 [![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.2587907.svg)](https://doi.org/10.5281/zenodo.2587907)
 [![Gitter chat](https://badges.gitter.im/gitterHQ/gitter.png)](https://gitter.im/gitterHQ/gitter)
+[![pre-commit.ci status](https://results.pre-commit.ci/badge/github/ssec/sift/master.svg)](https://results.pre-commit.ci/latest/github/ssec/sift/master)
 
 
 Satellite Information Familiarization Tool (SIFT) was designed by the Space
@@ -28,6 +29,21 @@ also be found on GitHub: https://github.com/ssec/sift/wiki
 
 Developer documentation can be found on https://sift.readthedocs.io/en/latest/.
 
+## History
+
+SIFT was originally created and designed at [SSEC/CIMSS at the University of
+Wisconsin - Madison](https://cimss.ssec.wisc.edu/) as a training tool for US
+NWS forecasters. Later, [EUMETSAT, European Organization for the Exploitation
+of Meteorological Satellites](https://www.eumetsat.int/),
+joined the project contributing many new features and refactoring various
+portions of the project to support instrument calibration/validation workflows
+as well as additional scientific analysis. CIMSS and EUMETSAT now work on the
+project together as well as accepting contributions from users outside these
+groups.
+
+EUMETSAT contributions, leading up to SIFT 2.0, were carried out by
+[ask – Innovative Visualisierungslösungen GmbH](https://askvisual.de/).
+
 ## Data Access and Reading
 
 SIFT uses the open source python library Satpy to read input data. By using

RELEASING.md

@@ -32,4 +32,3 @@ See [semver.org](http://semver.org/) on how to write a version number.
 7. Create a release of the package on
    [github](https://github.com/ssec/sift/releases) by drafting a new release
    and copying the release notes from the changelog (see above).
-