From 1d5747fe744d6e8aa2f613306a2341e4210b7449 Mon Sep 17 00:00:00 2001 From: Eleanor Frajka-Williams Date: Sat, 20 Sep 2025 21:58:56 +0200 Subject: [PATCH 1/3] Update links for new org --- CITATION.cff | 2 +- README.md | 14 +++++++------- docs/source/index.rst | 2 +- oceanarray/config/legacy/project_RAPID.yaml | 2 +- pyproject.toml | 6 +++--- tests/legacy/test_process_rodb.py | 5 +++-- tests/legacy/test_rodb.py | 6 +++--- 7 files changed, 19 insertions(+), 18 deletions(-) diff --git a/CITATION.cff b/CITATION.cff index 67999d3..383c81f 100644 --- a/CITATION.cff +++ b/CITATION.cff @@ -8,4 +8,4 @@ authors: title: oceanarray version: 0.0.1 date-released: 2025-06-07 -url: https://github.com/eleanorfrajka/oceanarray +url: https://github.com/ocean-uhh/oceanarray diff --git a/README.md b/README.md index 40b695b..ea19f5a 100644 --- a/README.md +++ b/README.md @@ -18,7 +18,7 @@ OceanArray processes raw oceanographic instrument data following CF conventions. ### Installation ```bash -git clone https://github.com/eleanorfrajka/oceanarray.git +git clone https://github.com/ocean-uhh/oceanarray.git cd oceanarray pip install -r requirements-dev.txt pip install -e . @@ -48,7 +48,7 @@ stage2.process_mooring('mooring_name') - Preserve all original data with standardized variable names and metadata - No quality control applied - pure format conversion -**Stage 2: Temporal Corrections** (`stage2.py`) +**Stage 2: Temporal Corrections** (`stage2.py`) - Apply clock offset corrections between instruments - Trim data to deployment period (start_time to end_time) - Add deployment metadata and processing provenance @@ -160,7 +160,7 @@ make html The documentation includes: - **Processing Methods**: Methodology for each stage -- **API Reference**: Function and class documentation +- **API Reference**: Function and class documentation - **Demo Notebooks**: Tutorials and examples - **Development Guide**: Roadmap and contribution guidelines @@ -170,7 +170,7 @@ The documentation includes: ### Current Support - **Sea-Bird SBE**: CNV and ASCII formats (`.cnv`, `.asc`) -- **RBR**: RSK and ASCII formats (`.rsk`, `.dat`) +- **RBR**: RSK and ASCII formats (`.rsk`, `.dat`) - **Nortek**: ASCII format with header files (`.aqd`) ### Planned Support @@ -189,7 +189,7 @@ pytest # With coverage pytest --cov=oceanarray -# Specific test categories +# Specific test categories pytest tests/test_stage1.py tests/test_stage2.py ``` @@ -256,7 +256,7 @@ If you use OceanArray in your research, please cite: @software{oceanarray, title = {{OceanArray}: A Python framework for oceanographic mooring array processing}, author = {Frajka-Williams, Eleanor}, - url = {https://github.com/eleanorfrajka/oceanarray}, + url = {https://github.com/ocean-uhh/oceanarray}, year = {2025} } -``` \ No newline at end of file +``` diff --git a/docs/source/index.rst b/docs/source/index.rst index 6c14ee0..ae206f9 100644 --- a/docs/source/index.rst +++ b/docs/source/index.rst @@ -57,7 +57,7 @@ Contents :maxdepth: 2 :caption: Help and reference - GitHub Repo + GitHub Repo roadmap oceanarray faq diff --git a/oceanarray/config/legacy/project_RAPID.yaml b/oceanarray/config/legacy/project_RAPID.yaml index bafb62c..7e336e1 100644 --- a/oceanarray/config/legacy/project_RAPID.yaml +++ b/oceanarray/config/legacy/project_RAPID.yaml @@ -19,7 +19,7 @@ creator_url: "https://www.noc.ac.uk" creator_institution: "National Oceanography Centre" creator_id: https://edmo.seadatanet.org/report/17 array: RAPID -comment: Data file in OS format produced using http://github.com/eleanorfrajka/oceanarray +comment: Data file in OS format produced using http://github.com/ocean-uhh/oceanarray sea_area: North Atlantic Ocean sea_area_vocabulary: https://vocab.nerc.ac.uk/collection/C19/current/ #geospatial_lat_min: diff --git a/pyproject.toml b/pyproject.toml index d052f66..51b5c53 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -26,9 +26,9 @@ dynamic = [ "dependencies", "version", ] -urls.documentation = "https://github.com/eleanorfrajka/oceanarray" -urls.homepage = "https://github.com/eleanorfrajka/oceanarray" -urls.repository = "https://github.com/eleanorfrajka/oceanarray" +urls.documentation = "https://github.com/ocean-uhh/oceanarray" +urls.homepage = "https://github.com/ocean-uhh/oceanarray" +urls.repository = "https://github.com/ocean-uhh/oceanarray" [tool.setuptools.packages.find] diff --git a/tests/legacy/test_process_rodb.py b/tests/legacy/test_process_rodb.py index 1583e34..3e606f6 100644 --- a/tests/legacy/test_process_rodb.py +++ b/tests/legacy/test_process_rodb.py @@ -67,6 +67,7 @@ def test_apply_microcat_with_flags(tmp_path): # Patch rodbload to return this dataset import oceanarray.legacy.process_rodb as process_rodb + process_rodb.rodb.rodbload = lambda _: ds ds_cal = apply_microcat_calibration_from_txt(txt, use_path) @@ -85,7 +86,7 @@ def test_apply_microcat_calibration_from_txt(tmp_path): data_dir = Path(__file__).parent.parent / "data" txt_file = data_dir / "wb1_12_2015_005.microcat.txt" use_file = data_dir / "wb1_12_2015_6123.use" - + if not txt_file.exists() or not use_file.exists(): pytest.skip("Legacy test data files not available") @@ -103,7 +104,7 @@ def test_apply_microcat_calibration_from_txt(tmp_path): def test_stage2_trim_from_raw(tmp_path): data_dir = Path(__file__).parent.parent / "data" raw_file = data_dir / "wb1_12_2015_6123.raw" - + if not raw_file.exists(): pytest.skip("Legacy test data files not available") diff --git a/tests/legacy/test_rodb.py b/tests/legacy/test_rodb.py index de8d013..7352280 100644 --- a/tests/legacy/test_rodb.py +++ b/tests/legacy/test_rodb.py @@ -38,10 +38,10 @@ def test_rodbload_missing_time(tmp_path, caplog): def test_rodbload_raw_file(): file_path = Path(__file__).parent.parent / "data" / "wb1_12_2015_6123.raw" - + if not file_path.exists(): pytest.skip("Legacy test data files not available") - + variables = ["YY", "MM", "DD", "HH", "T", "C", "P"] ds = rodbload(file_path, variables) @@ -83,7 +83,7 @@ def test_format_latlon(): def test_rodb_read_write_roundtrip(): infile = Path(__file__).parent.parent / "data" / "wb1_12_2015_6123_head10.use" - + if not infile.exists(): pytest.skip("Legacy test data files not available") From d4d55c7f51baccddb27980154bee0fb81f13ebf8 Mon Sep 17 00:00:00 2001 From: Eleanor Frajka-Williams Date: Sat, 20 Sep 2025 22:02:01 +0200 Subject: [PATCH 2/3] Update docs/source/index.rst Co-authored-by: Copilot <175728472+Copilot@users.noreply.github.com> --- docs/source/index.rst | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/docs/source/index.rst b/docs/source/index.rst index ae206f9..843c494 100644 --- a/docs/source/index.rst +++ b/docs/source/index.rst @@ -57,7 +57,7 @@ Contents :maxdepth: 2 :caption: Help and reference - GitHub Repo + GitHub Repo roadmap oceanarray faq From 09ac9a9985ef6197261f6b4863b76bab61e93be4 Mon Sep 17 00:00:00 2001 From: Eleanor Frajka-Williams Date: Sat, 20 Sep 2025 22:02:13 +0200 Subject: [PATCH 3/3] Update oceanarray/config/legacy/project_RAPID.yaml Co-authored-by: Copilot <175728472+Copilot@users.noreply.github.com> --- oceanarray/config/legacy/project_RAPID.yaml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/oceanarray/config/legacy/project_RAPID.yaml b/oceanarray/config/legacy/project_RAPID.yaml index 7e336e1..9629448 100644 --- a/oceanarray/config/legacy/project_RAPID.yaml +++ b/oceanarray/config/legacy/project_RAPID.yaml @@ -19,7 +19,7 @@ creator_url: "https://www.noc.ac.uk" creator_institution: "National Oceanography Centre" creator_id: https://edmo.seadatanet.org/report/17 array: RAPID -comment: Data file in OS format produced using http://github.com/ocean-uhh/oceanarray +comment: Data file in OS format produced using https://github.com/ocean-uhh/oceanarray sea_area: North Atlantic Ocean sea_area_vocabulary: https://vocab.nerc.ac.uk/collection/C19/current/ #geospatial_lat_min: