Merge pull request #427 from dbekaert/dev

Release: v0.2.0

.circleci/config.yml

@@ -0,0 +1,63 @@
+version: 2.1
+jobs:
+  build:
+    docker:
+      - image: cimg/base:current
+        user: root
+    steps:
+      - checkout
+      - run:
+          name: Setup micromamba
+          command: |
+            apt update --yes && apt-get upgrade --yes
+            apt install -y --no-install-recommends wget ca-certificates git
+            cd $HOME
+            curl -Ls https://micro.mamba.pm/api/micromamba/linux-64/latest | tar -xvj bin/micromamba
+
+      - run:
+          name: Setup environment
+          command: |
+            eval "$($HOME/bin/micromamba shell hook -s posix)"
+            micromamba create -f environment.yml
+            micromamba activate RAiDER
+            pip install coveralls
+            echo url: https://cds.climate.copernicus.eu/api/v2 > $HOME/.cdsapirc
+            echo key: $cdsak >> $HOME/.cdsapirc
+         
+            echo { > $HOME/.ecmwfapirc
+            echo '  "url": "https://api.ecmwf.int/v1",' >> $HOME/.ecmwfapirc
+            echo '  "email": "'$ecmwfu'",' >> $HOME/.ecmwfapirc
+            echo '  "key": "'$ecmwfk'"' >> $HOME/.ecmwfapirc
+            echo } >> $HOME/.ecmwfapirc
+
+            echo url: $NCUMloc > $HOME/.ncmrlogin
+            echo username: $NCUMu >> $HOME/.ncmrlogin
+            echo password: $NCUMp >> $HOME/.ncmrlogin
+
+            python --version
+            python -c "import numpy; print(numpy.__version__)"
+            python -c "import pyproj; print(pyproj.__version__)"
+      - run:
+          name: Install RAiDER and test the install
+          command: |
+            eval "$($HOME/bin/micromamba shell hook -s posix)"
+            micromamba activate RAiDER
+            python -m pip install .
+            python -c "import RAiDER; from RAiDER.delay import main"
+            python -c "import RAiDER; from RAiDER.interpolator import interp_along_axis"
+      - run:
+          name: Run unit tests
+          shell: /bin/bash -l
+          command: |
+            eval "$($HOME/bin/micromamba shell hook -s posix)"
+            micromamba activate RAiDER
+            COV_OPTIONS=`python -c "import importlib;print(*(' --cov='+p for p in importlib.util.find_spec('RAiDER').submodule_search_locations))"`
+            pytest -m "not long" test/ $COV_OPTIONS --cov-report=
+      - run:
+          name: Report coverage
+          command: |
+            eval "$($HOME/bin/micromamba shell hook -s posix)"
+            micromamba activate RAiDER
+            python .circleci/fix_coverage_paths.py .coverage $(pwd)/tools/RAiDER/
+            coverage report -mi
+            coveralls

.circleci/fix_coverage_paths.py

@@ -0,0 +1,23 @@
+import re
+import sqlite3
+import sys
+
+
+def main(file, replacement):
+    conn = sqlite3.connect(file)
+    cur = conn.cursor()
+    cur.execute("select path, id from file")
+
+    patched = [
+        (re.sub(r"/.*/RAiDER/", replacement, r[0]), r[1])
+        for r in cur
+    ]
+
+    cur.executemany("update file set path=? where id=?", patched)
+
+    conn.commit()
+    conn.close()
+
+
+if __name__ == '__main__':
+    main(*sys.argv[1:])

.github/ISSUE_TEMPLATE/bug_report.md

@@ -0,0 +1,30 @@
+---
+name: Bug report
+about: Create a report to help us improve
+title: "[BUG]"
+labels: bug
+assignees: ''
+
+---
+
+**Describe the bug**
+A clear and concise description of what the bug is.
+
+**To Reproduce**
+Steps to reproduce the behavior:
+1. Download 
+2. Command used
+3. Error Output
+
+**Expected behavior**
+A clear and concise description of what you expected to happen.
+
+**Screenshots**
+If applicable, add screenshots to help explain your problem.
+
+**Desktop (please complete the following information):**
+ - RAiDER git tag: [e.g. git show --summary]
+ - OS
+
+**Additional context**
+Add any other context about the problem her

.github/dependabot.yml

@@ -0,0 +1,7 @@
+version: 2
+updates:
+  - package-ecosystem: "github-actions"
+    directory: "/"
+    schedule:
+      # Check for updates to GitHub Actions every weekday
+      interval: "weekly"

.github/pull_request_template.md

@@ -0,0 +1,39 @@
+<!--- Provide a general summary of your changes in the Title above -->
+
+## Description
+<!--- Describe your changes in detail -->
+
+## Motivation and Context
+<!--- Why is this change required? What problem does it solve? -->
+<!--- If it fixes an open issue, please link to the issue here. -->
+
+## How Has This Been Tested?
+<!--- Please run the following command on your PR to ensure code formatting consistency: -->
+<!--- autopep8 <changed files/folders> --recursive --in-place --ignore=E5 -->
+
+<!--- Please describe how you tested your changes. -->
+
+
+<!--- For new functionality, describe added unit tests. -->
+
+
+<!--- If this PR breaks existing unit tests, please describe in detail -->
+<!--- which tests break and why. Describe what functionality is changed. -->
+
+
+## Screenshots (if appropriate):
+
+## Type of change
+<!--- What types of changes does your code introduce? Put an `x` in all the boxes that apply: -->
+- [ ] Bug fix (non-breaking change which fixes an issue)
+- [ ] New feature (non-breaking change which adds functionality)
+- [ ] Breaking change (fix or feature that would cause existing functionality to not work as expected)
+
+## Checklist:
+<!--- Go over all the following points, and put an `x` in all the boxes that apply. -->
+<!--- If you're unsure about any of these, don't hesitate to ask. We're here to help! -->
+- [ ] I have added an explanation of what your changes do and why you'd like us to include them.
+- [ ] I have written new tests for your core changes, as applicable.
+- [ ] I have successfully ran tests with your changes locally.
+- [ ] My change requires a change to the documentation.
+- [ ] I have updated the documentation accordingly.

.github/workflows/build.yml

@@ -0,0 +1,29 @@
+name: Docker Build
+
+on:
+  push:
+    branches:
+      - main
+      - dev
+  pull_request:
+    branches:
+      - main
+      - dev
+
+jobs:
+  call-version-info-workflow:
+    uses: ASFHyP3/actions/.github/workflows/reusable-version-info.yml@v0.6.0
+    with:
+      conda_env_name: RAiDER
+      python_version: '3.10'
+
+  call-docker-ghcr-workflow:
+    needs: call-version-info-workflow
+    uses: ASFHyP3/actions/.github/workflows/reusable-docker-ghcr.yml@v0.6.0
+    with:
+      version_tag: ${{ needs.call-version-info-workflow.outputs.version_tag }}
+      release_branch: main
+      develop_branch: dev
+      user: ${{ github.actor }}
+    secrets:
+      USER_TOKEN: ${{ secrets.GITHUB_TOKEN }}

.github/workflows/changelog.yml

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+name: Changelog updated?
+
+on:
+  pull_request:
+    types:
+      - opened
+      - labeled
+      - unlabeled
+      - synchronize
+    branches:
+      - main
+      - dev
+
+jobs:
+  call-changelog-check-workflow:
+    uses: ASFHyP3/actions/.github/workflows/reusable-changelog-check.yml@v0.6.0
+    secrets:
+      USER_TOKEN: ${{ secrets.GITHUB_TOKEN }}

.github/workflows/labeled-pr.yml

@@ -0,0 +1,15 @@
+name: Is PR labeled?
+
+on:
+  pull_request:
+    types:
+      - opened
+      - labeled
+      - unlabeled
+      - synchronize
+    branches:
+      - main
+
+jobs:
+  call-labeled-pr-check-workflow:
+    uses: ASFHyP3/actions/.github/workflows/reusable-labeled-pr-check.yml@v0.6.0

.github/workflows/release.yml

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+name: Create Release
+
+on:
+  push:
+    tags:
+      - 'v*'
+
+jobs:
+  call-release-workflow:
+    uses: ASFHyP3/actions/.github/workflows/reusable-release.yml@v0.6.0
+    with:
+      release_prefix: RAiDER
+      develop_branch: dev
+      sync_pr_label: bot
+    secrets:
+      USER_TOKEN: ${{ secrets.RELEASE_ACCESS_TOKEN }}

.github/workflows/tag.yml

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+name: Tag version
+
+on:
+  push:
+    branches:
+      - main
+
+jobs:
+  call-bump-version-workflow:
+    uses: ASFHyP3/actions/.github/workflows/reusable-bump-version.yml@v0.6.0
+    with:
+      user: dbekaert
+      email: bekaertdavid@gmail.com
+    secrets:
+      USER_TOKEN: ${{ secrets.RELEASE_ACCESS_TOKEN }}

.gitignore

@@ -1,7 +1,26 @@
-*.swp
 __pycache__
+.vscode
+*.pyc
+*~
+*.swp
+*.DS_Store
+.ftpignore
+.ftpconfig
+.ipynb_checkpoints
+build
+*.so
+*.cmake
+CMake*
+Makefile
+dummy*
+weather_files
+test/data
 *.log
-test/ERA*
-*.dat
 *.pdf
-*.pyc
+*.cpp
+test/*/geom/*.dem
+test/*/geom/*.nc
+.eggs/
+dist/
+tools/RAiDER.egg-info/
+tools/bindings/utils/makePoints.c