v0.6.0 #766

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Merged

jlmaurer merged 164 commits into main from dev

Sep 9, 2025

.circleci/conda-lock-3.10.yml

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.circleci/conda-lock-3.11.yml

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.circleci/conda-lock-3.12.yml

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.circleci/conda-lock-3.9.yml

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.circleci/config.yml

            
                      Original file line number
                      Diff line number
                      Diff line change
                  
    @@ -13,37 +13,46 @@ jobs:
  
          - run:

              name: Install MiniForge

              shell: /bin/bash -l

              shell: /bin/bash -xl

              command: |

                apt update --yes && apt-get upgrade --yes

                apt install -y --no-install-recommends wget ca-certificates git

                apt update --yes && apt upgrade --yes

                apt install --yes --no-install-recommends wget ca-certificates git

                cd ${HOME}

                wget -O  Miniforge3.sh "https://github.com/conda-forge/miniforge/releases/latest/download/Miniforge3-$(uname)-$(uname -m).sh"

                wget -O Miniforge3.sh \

                  "https://github.com/conda-forge/miniforge/releases/latest/download/Miniforge3-$(uname)-$(uname -m).sh"

                bash Miniforge3.sh -b -p "${HOME}/conda"

                source "${HOME}/conda/etc/profile.d/conda.sh"

                source "${HOME}/conda/etc/profile.d/mamba.sh"

                # Put mamba's shell init into a profile.d file, in order to activate

                # it even in non-interactive terminals

                "${HOME}/conda/bin/mamba" shell hook --shell bash --root-prefix "${HOME}/conda" \

                  > /etc/profile.d/mamba-raider-circleci.sh

          - run:

              name: Install conda-lock

              shell: /bin/bash -xl

              command: |

                mamba install --channel=conda-forge --name=base conda-lock

          - run:

              name: Create RAiDER environment

              no_output_timeout: 30m

              no_output_timeout: 60m

              shell: /bin/bash -xl

              command: |

                source "${HOME}/conda/etc/profile.d/conda.sh"

                source "${HOME}/conda/etc/profile.d/mamba.sh"

                PYTHON_VERSION="<< parameters.python-version >>"

                sed -i "/python>=/c\ - python=${PYTHON_VERSION}" environment.yml

                mamba env create -f environment.yml

                if [ "${PYTHON_VERSION}" == "3.13" ]; then

                  LOCKFILE_PATH="conda-lock.yml"

                else

                  LOCKFILE_PATH=".circleci/conda-lock-${PYTHON_VERSION}.yml"

                fi

                mamba activate base

                conda-lock install --prefix "${HOME}/conda/envs/RAiDER" "${LOCKFILE_PATH}"

                echo "mamba activate RAiDER" >> /etc/profile.d/mamba-raider-circleci.sh

          - run:

              name: Install raider and check environment

              name: Install RAiDER and check environment

              shell: /bin/bash -xl

              command: |

                source "${HOME}/conda/etc/profile.d/conda.sh"

                source "${HOME}/conda/etc/profile.d/mamba.sh"

                mamba activate RAiDER

                python -m pip install --no-deps .

                python -c "import RAiDER; from RAiDER.delay import tropo_delay"

    @@ -54,36 +63,25 @@ jobs:
  
                python -c "import pyproj; print(pyproj.__version__)"

          - run:

              name: Setup data stores

              name: Set up data stores

              shell: /bin/bash -xl

              command: |

                source "${HOME}/conda/etc/profile.d/conda.sh"

                source "${HOME}/conda/etc/profile.d/mamba.sh"

                mamba activate RAiDER

                python -c 'from RAiDER.models.credentials import setup_from_env; setup_from_env()'

          - run:

              name: Run unit tests

              shell: /bin/bash -xl

              command: |

                source "${HOME}/conda/etc/profile.d/conda.sh"

                source "${HOME}/conda/etc/profile.d/mamba.sh"

                mamba activate RAiDER

                COV_OPTIONS=`python -c "import importlib;print(*(' --cov='+p for p in importlib.util.find_spec('RAiDER').submodule_search_locations))"`

                coverage run -m pytest -m "not long" test/ ${COV_OPTIONS} --cov-report=

                python -m pip install pytest-cov

                COV_OPTIONS=`python -c "import importlib.util; 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

              shell: /bin/bash -xl

              command: |

                PYTHON_VERSION="<< parameters.python-version >>"

                if [ "${PYTHON_VERSION}" == "3.12" ]; then

                  source "${HOME}/conda/etc/profile.d/conda.sh"

                  source "${HOME}/conda/etc/profile.d/mamba.sh"

                  mamba activate RAiDER

                if [ "${PYTHON_VERSION}" == "3.13" ]; then

                  python -m pip install coveralls

                  python .circleci/fix_coverage_paths.py .coverage ${PWD}/tools/RAiDER/

                  coverage report -mi --show-missing --data-file=.coverage

    @@ -96,4 +94,4 @@ workflows:
  
          - build:

              matrix:

                parameters:

                  python-version: ["3.9", "3.10", "3.11", "3.12"]

                  python-version: ["3.9", "3.10", "3.11", "3.12", "3.13"]

.circleci/regenerate-locks.py

-Original file line number
+Diff line change
@@ -0,0 +1,65 @@
+    """
+    Script to assist in regenerating each Python version's lockfiles after making
+    changes to environment.yml.
+    """
+    import re
+    import subprocess
+    import tempfile
+    from pathlib import Path
+    import yaml
+    from tqdm import tqdm
+    from RAiDER.logger import logger
+    # Matches the "dependencies" entry for python.
+    # First group: like " - python"
+    # Second group: like ">=3.8"
+    PATTERN_PYTHON_DEP = re.compile(r'^(\s*-\s*python)([<>=~]?=?.+)$', re.MULTILINE)
+    def generate_lock(out_path: Path, version: str, template: str) -> None:
+        """
+        Use conda-lock to generate a lockfile for this version of the
+        environment.yml file, and place it at the specified output path.
+        """
+        logger.info(f'Generating lockfile for Python {version}...')
+        with tempfile.TemporaryDirectory() as tmp_dir_str:
+            env_path = Path(tmp_dir_str) / 'environment.yml'
+            # Hardcode a copy of the environment.yml file to this Python version
+            with env_path.open('w', encoding='utf-8') as f_env:
+                f_env.write(re.sub(PATTERN_PYTHON_DEP, f'\\1={version}', template))
+            # Platforms explicitly listed in order to exclude win-64, since isce3
+            # and wand (and therefore RAiDER) are not compatible with Windows.
+            cmd = f'conda-lock -f {env_path} --lockfile {out_path} -p linux-64 -p osx-64 -p osx-arm64'
+            logger.debug(f'>>> {cmd}')
+            result = subprocess.run(cmd.split(' '), stdout=subprocess.PIPE, text=True)
+            if result.returncode != 0:
+                raise Exception(f'Command exited with non-zero status {result.returncode}: "{cmd}"')
+    def main() -> None:
+        """(Re)generates a lockfile for each Python version in .circleci/config.yml."""
+        with Path('environment.yml').open(encoding='utf-8') as f_env:
+            yml_content = f_env.read()
+        # Read RAiDER's supported Python versions from CircleCI config.
+        # The last entry in the list will be placed in the project root.
+        with Path('.circleci/config.yml').open(encoding='utf-8') as f_ci_config:
+            versions: list[str] = yaml.safe_load(f_ci_config) \
+                ['workflows']['all-tests']['jobs'][0] \
+                ['build']['matrix']['parameters']['python-version']
+        for i, version in tqdm(enumerate(versions), total=len(versions), unit='lockfiles written'):
+            if i < len(versions) - 1:
+                generate_lock(Path(f'.circleci/conda-lock-{version}.yml'), version, yml_content)
+            else:
+                generate_lock(Path('conda-lock.yml'), version, yml_content)
+    if __name__ == '__main__':
+        main()

.github/dependabot.yml

-Original file line number
+Diff line change
@@ Expand Up / @@ -5,3 +5,5 @@ updates: @@
         schedule:
           # Check for updates to GitHub Actions every weekday
           interval: "weekly"
+        labels:
+          - bumpless

.github/workflows/build.yml

-Original file line number
+Diff line change
@@ Expand Up / @@ -3,26 +3,30 @@ name: Docker Build @@
     on:
       push:
         branches:
-          - main
           - dev
+        tags:
+          - 'v*'
       pull_request:
         branches:
           - main
           - dev
     jobs:
       call-version-info-workflow:
-        uses: ASFHyP3/actions/.github/workflows/reusable-version-info.yml@v0.17.1
+        uses: ASFHyP3/actions/.github/workflows/reusable-version-info.yml@v0.20.0
+        permissions:
+          contents: read
         with:
           python_version: '3.10'
       call-docker-ghcr-workflow:
         needs: call-version-info-workflow
-        uses: ASFHyP3/actions/.github/workflows/reusable-docker-ghcr.yml@v0.17.1
+        uses: ASFHyP3/actions/.github/workflows/reusable-docker-ghcr.yml@v0.20.0
+        permissions:
+          contents: read
+          packages: write
         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

-Original file line number
+Diff line change
@@ Expand Up / @@ -13,4 +13,6 @@ on: @@
     jobs:
       call-changelog-check-workflow:
-        uses: ASFHyP3/actions/.github/workflows/reusable-changelog-check.yml@v0.17.1
+        uses: ASFHyP3/actions/.github/workflows/reusable-changelog-check.yml@v0.20.0
+        permissions:
+          contents: read

.github/workflows/deploy-docs.yml

            
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                      Diff line change
                  
    @@ -10,13 +10,14 @@ jobs:
  
        name: Build site and deploy

        runs-on: "ubuntu-latest"

        steps:

          - uses: actions/checkout@v4

          - uses: actions/checkout@v5

            with:

              fetch-depth: 0

          - uses: mamba-org/provision-with-micromamba@v16

          - uses: mamba-org/setup-micromamba@v2

            with:

              extra-specs: |

              environment-file: environment.yml

              create-args: >-

                python=3.10

          - name: install RAiDER

.github/workflows/labeled-pr.yml

-Original file line number
+Diff line change
@@ Expand Up / @@ -12,4 +12,6 @@ on: @@
     jobs:
       call-labeled-pr-check-workflow:
-        uses: ASFHyP3/actions/.github/workflows/reusable-labeled-pr-check.yml@v0.17.1
+        uses: ASFHyP3/actions/.github/workflows/reusable-labeled-pr-check.yml@v0.20.0
+        permissions:
+          pull-requests: read

.github/workflows/release.yml

-Original file line number
+Diff line change
@@ Expand Up / @@ -7,10 +7,11 @@ on: @@
     jobs:
       call-release-workflow:
-        uses: ASFHyP3/actions/.github/workflows/reusable-release.yml@v0.17.1
+        uses: ASFHyP3/actions/.github/workflows/reusable-release.yml@v0.20.0
+        permissions: {}
         with:
           release_prefix: RAiDER
           develop_branch: dev
-          sync_pr_label: bot
+          sync_pr_label: bumpless
         secrets:
           USER_TOKEN: ${{ secrets.RELEASE_ACCESS_TOKEN }}

.github/workflows/tag.yml

-Original file line number
+Diff line change
@@ Expand Up / @@ -7,7 +7,8 @@ on: @@
     jobs:
       call-bump-version-workflow:
-        uses: ASFHyP3/actions/.github/workflows/reusable-bump-version.yml@v0.17.1
+        uses: ASFHyP3/actions/.github/workflows/reusable-bump-version.yml@v0.20.0
+        permissions: {}
         with:
           user: dbekaert
           email: bekaertdavid@gmail.com
@@ Expand Down @@

.gitignore

-Original file line number
+Diff line change
@@ Expand Up / @@ -26,3 +26,12 @@ test/GUNW/ @@
     dist/
     tools/RAiDER.egg-info/
     tools/bindings/utils/makePoints.c
+    gunw_azimuth_test_data/
+    test/synthetic_test/*.nc
+    test/synthetic_test/weather_files_synth/
+    orbits/
+    .lsp/
+    /*.nc
+    /GUNW*.yaml
+    /*.tif
+    .coverage*

CHANGELOG.md

-Original file line number
+Diff line change
@@ Expand Up @@
     and this project adheres to [PEP 440](https://www.python.org/dev/peps/pep-0440/)
     and uses [Semantic Versioning](https://semver.org/spec/v2.0.0.html).
+    ## [0.6.0]
+    ### Removed
+    * [764](https://github.com/dbekaert/RAiDER/pull/764) - Removed Python 3.8 support. Python 3.9 is now the minimum version officially required to run RAiDER.
+    * [753](https://github.com/dbekaert/RAiDER/pull/753) - Removed support for ERA-Interim.
+    ### Changed
+    * [743](https://github.com/dbekaert/RAiDER/pull/743) - Switched from HTTPS to DAP4 for retrieving MERRA2 data, and suppressed a warning for using DAP4 for GMAO data where doing so is not possible.
+    ### Fixed
+    * [765](https://github.com/dbekaert/RAiDER/pull/765) - Fixed a dead link to "Installing from Source" in the ReadMe.
+    * [759](https://github.com/dbekaert/RAiDER/pull/759) - Added a `browse` S3 tag for `.png` files when uploaded to AWS.
+    * [751](https://github.com/dbekaert/RAiDER/pull/751) - Fixed ERA-5 interface for a change to its API that requires pressure variables to be requested separately from temperature and humidity.
+    * [741](https://github.com/dbekaert/RAiDER/pull/741) - Updated mamba setup commands in CircleCI for mamba 2.0.0.
+    * [738](https://github.com/dbekaert/RAiDER/pull/738) - Resolved an InsecureRequestWarning when fetching data through CDS, such as for ERA5.
+    * [734](https://github.com/dbekaert/RAiDER/pull/734) - Resolved a deprecation warning from Rasterio about the use of `statistics()`.
+    * [733](https://github.com/dbekaert/RAiDER/pull/733) - Fixed coverage reports being generated for incorrect directories.
+    * [732](https://github.com/dbekaert/RAiDER/pull/732) - Updated `hrrr.py` to resolve a deprecation warning about `unary_union`.
+    * [731](https://github.com/dbekaert/RAiDER/pull/731) - Fixed fetch routine for GMAO.
+    ### Added
+    * [762](https://github.com/dbekaert/RAiDER/pull/762) - Added lockfiles through conda-lock to the repo, documentation, and CircleCI runners.
+    * [761](https://github.com/dbekaert/RAiDER/pull/761) - Added Python 3.13 support.
+    * [747](https://github.com/dbekaert/RAiDER/pull/747) - Added support for run config time format `%H:%M:%S` (without quotes).
+    * [746](https://github.com/dbekaert/RAiDER/pull/746) - Added support for numpy v2.
+    * [725](https://github.com/dbekaert/RAiDER/pull/725) - Added rules to ignore all test artifacts in git.
+    * [728](https://github.com/dbekaert/RAiDER/pull/728) - Added downloader tests for HRES, GMAO, and MERRA2.
+    * [726](https://github.com/dbekaert/RAiDER/pull/726) - Updated code and documentation for changes to the CDS API.
     ## [0.5.5]
     ### Changed
     * `RAiDER.s1_orbits` now uses the `s1_orbits` package to retrieve orbit files from AWS, rather than using `hyp3lib`
@@ Expand Down @@

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