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Updates to improve compliance with the IOOS Compliance Checker (glide… #163

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Updates to improve compliance with the IOOS Compliance Checker (glide… #163

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Commits on Mar 26, 2024

  1. Updates to improve compliance with the IOOS Compliance Checker (glide… 

    …rdac:3.0)

 * Still need to ignore `ancillary_variable` recommendations
 * ncprocess.py
   * profile_id: Max int32 type; attributes valid max and min also need to be same type; _FillValue = -999
   * platform: Max int32 type; _FillValue = -999
   * set time encoding to float to avoid UserWarnings about time conversion
 * slocum.py
   * If import test fails for dbdreader, the flag should be False for have_dbdreader?
   * Need pandas to help avoid UserWarnings about time conversion; set encoding to float for time encoding
   * depth: valid min/max and _FillValue updates to match gliderdac:3.0
   * Other updates from char to float to match gliderdac:3.0
   * Obtain direct version of libnetcdf (borrow code from xarray)
 * tests
   * Add README to discover location of example data

Other things that should be added/updated to respective deployment.yml files to improve
compliance.  Once that is done, things are squeaky clean.

```
$ compliance-checker -t gliderdac:3.0 -s check_ancillary_variables pyglider/L0-profiles/unit507-20240325T1507.nc
Running Compliance Checker on the datasets from: ['pyglider/L0-profiles/unit507-20240325T1507.nc']

--------------------------------------------------------------------------------
                         IOOS Compliance Checker Report
                                Version unknown
                     Report generated 2024-03-26T00:50:22Z
                                 gliderdac:3.0
      https://ioos.github.io/glider-dac/ngdac-netcdf-file-format-version-2
--------------------------------------------------------------------------------
All tests passed!
```
    @jr3cermak
    jr3cermak committed Mar 26, 2024
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Commits on Apr 5, 2024

  1. TST: add 3.9 back in

    @jklymak
    jklymak committed Apr 5, 2024
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Commits on Apr 18, 2024

  1. MNT: more time changes - seconds to nano

    C-PROOF committed Apr 18, 2024
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Commits on Apr 26, 2024

  1. ENH: make time Fill Value show up in NetCDF via encoding

    @jklymak
    jklymak committed Apr 26, 2024
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Commits on Apr 29, 2024

  1. ENH: Fill Value

    @jklymak
    jklymak committed Apr 29, 2024
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Commits on May 20, 2024

  1. FIX: time in profiles

    C-PROOF committed May 20, 2024
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Commits on May 21, 2024

  1. ENH: add startime

    C-PROOF committed May 21, 2024
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Commits on May 26, 2024

  1. FIX: make get_depth more robust to missing data

    C-PROOF committed May 26, 2024
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  2. FIX: make get_derived_eos_raw more robust to no locations

    C-PROOF committed May 26, 2024
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Commits on Jun 1, 2024

  1. FIX: bad maxgap default

    @jklymak
    jklymak committed Jun 1, 2024
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  2. Merge pull request c-proof#169 from jklymak/fix-maxgap 

    FIX: bad maxgap default
    @jklymak
    jklymak authored Jun 1, 2024
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Commits on Jul 4, 2024

  1. ENH: allow multiple deploymentyaml

    C-PROOF committed Jul 4, 2024
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Commits on Jul 11, 2024

  1. Changed variable metadata to float

    @cassandra-elmer
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  2. Changed variable metadata to float

    @cassandra-elmer
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  3. Fix polars read_csv separator keyword

    @cassandra-elmer
    cassandra-elmer authored Jul 11, 2024
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  4. Fix str method strptime format keyword

    @cassandra-elmer
    cassandra-elmer authored Jul 11, 2024
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  5. Fix polars with_columns (using keep_name)

    @cassandra-elmer
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  6. Fix polars with_columns (using name.keep)

    @cassandra-elmer
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  7. Revert variable metadata to string

    @cassandra-elmer
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  8. Change variable metadata to float

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  9. Change variable metadata to float

    @cassandra-elmer
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  10. Revert variable metadata to string

    @cassandra-elmer
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  11. Change variable metadata to float

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  12. Change variable metadata to float

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  13. Change variable metadata to float

    @cassandra-elmer
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  14. Change variable metadata to float

    @cassandra-elmer
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  15. Add back required variable attributes as empty

    @cassandra-elmer
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  16. Add back required variable attributes as empty

    @cassandra-elmer
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  17. Add back required variable attributes as empty

    @cassandra-elmer
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  18. Add back required variable attributes as empty

    @cassandra-elmer
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  19. Change variable attr to float

    @cassandra-elmer
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  20. Change minimum density

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  21. Change minimum density

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  22. Change minimum density

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  23. Change minimum density

    @cassandra-elmer
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  24. Change variable attrs to float

    @cassandra-elmer
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  25. Change minimum density

    @cassandra-elmer
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  26. Change variable metadata to float

    @cassandra-elmer
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  27. Ensure Path variables are input to functions as str

    @cassandra-elmer
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Commits on Jul 12, 2024

  1. Revert unnecessary Path to str changes

    @cassandra-elmer
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Commits on Jul 14, 2024

  1. Merge pull request c-proof#173 from cassandra-elmer/fix_tests 

    Fix tests to passing
    @jklymak
    jklymak authored Jul 14, 2024
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  2. TST: update slocum (c-proof#175) 

    * FIX: improve CF and gliderdac compliance; add tests
    @jklymak
    jklymak authored Jul 14, 2024
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  3. FIX: fix NaN in u, v (c-proof#176) 

    Co-authored-by: C-PROOF <[email protected]>
    @jklymak
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Commits on Jul 17, 2024

  1. FIX: make times floatingpoint seconds, not integer seconds

    @jklymak
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  2. Merge pull request c-proof#177 from jklymak/fix-times-again 

    FIX: make times floating point seconds, not integer seconds
    @jklymak
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Commits on Jul 18, 2024

  1. FIX: time for profiles

    @jklymak
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  2. Merge pull request c-proof#178 from jklymak/fix-times-profiles 

    FIX: time for profiles
    @jklymak
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Commits on Jul 26, 2024

  1. standarise time encoding to seconds since 1970

    @callumrollo
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  2. Merge pull request c-proof#180 from voto-ocean-knowledge/dev 

    FIX: standarise time encoding to float seconds since 1970
    @jklymak
    jklymak authored Jul 26, 2024
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  3. FIX: for CF compliance

    @jklymak
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  4. ENH: make more cf compliant

    @jklymak
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  5. TST: fix timeseries

    @jklymak
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  6. Merge pull request c-proof#181 from jklymak/fix-cf-cmpliance 

    Fix cf compliance
    @jklymak
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Commits on Aug 6, 2024

  1. move to stable polars, pin numpy below 2

    @callumrollo
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  2. github expand test matrix and refresh cache

    @callumrollo
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  3. move tests to micromamba

    @callumrollo
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  4. REF: np.NaN >> np.nan. unpin numpy

    @callumrollo
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  5. Merge pull request c-proof#183 from voto-ocean-knowledge/requirements

    @jklymak
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  6. Merge branch 'main' into ci-micromamba

    @callumrollo
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  7. update checkout and codecov to recent supported versions

    @callumrollo
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Commits on Aug 7, 2024

  1. Merge pull request c-proof#184 from voto-ocean-knowledge/ci-micromamba 

    move tests to micromamba and update gh-actions versions
    @jklymak
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Commits on Aug 8, 2024

  1. FIX: make mission number int32

    cproof committed Aug 8, 2024
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  2. FIX: some more small things

    cproof committed Aug 8, 2024
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  3. Merge pull request c-proof#185 from c-proof/fix-mission-number 

    Fix mission number
    @jklymak
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Commits on Aug 13, 2024

  1. ENH: add more log decodng variables

    cproof committed Aug 13, 2024
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  2. Merge pull request c-proof#186 from c-proof/enh-more-log-decode 

    ENH: add more log decodng variables
    @jklymak
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  3. ENH: slocum - don't find profile indices if profile_min_time or profi… 

    …le_filt_time are None
    cproof committed Aug 13, 2024
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  4. Merge pull request c-proof#187 from c-proof/enh-skip-profiles 

    ENH: slocum - don't find profile indices if profile_min_time or profi…
    @jklymak
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Commits on Aug 31, 2024

  1. Check for pressure

    cproof committed Aug 31, 2024
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  2. FIX: yaml files: degrees to rad

    @jklymak
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  3. TST: fix the tests

    @jklymak
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  4. Merge pull request c-proof#189 from jklymak/fix-rad-degrees 

    Fix rad degrees
    @jklymak
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Commits on Sep 22, 2024

  1. MNT: pypi workflow

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  2. Merge pull request c-proof#192 from jklymak/pypi-workflow 

    MNT: pypi workflow
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  3. DOC: minor change to test pypi workflow

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  4. Merge pull request c-proof#193 from jklymak/test-pypi 

    DOC: minor change to test pypi workflow
    @jklymak
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  5. DOC: minor change to test pypi workflow

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  6. Merge pull request c-proof#194 from jklymak/test-pypi 

    DOC: minor change to test pypi workflow
    @jklymak
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  7. MNT: version change

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  8. Merge pull request c-proof#195 from jklymak/version-change 

    MNT: version change 0.0.7
    @jklymak
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  9. MNT: version change

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  10. Merge pull request c-proof#196 from jklymak/fix-version 

    MNT: version change
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  11. MNT

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  12. Merge pull request c-proof#197 from jklymak/fix-version2 

    MNT
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Commits on Oct 28, 2024

  1. DOC: fixes

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  2. Merge pull request c-proof#201 from jklymak/fix-example-data-link 

    DOC: fix data link in slocum desc
    @jklymak
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  3. DOC: RTD

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  4. Merge pull request c-proof#202 from jklymak/fix-read-the-docs 

    DOC: RTD
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Commits on Oct 29, 2024

  1. FIX

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  2. Merge pull request c-proof#203 from jklymak/fix-read-the-docs 

    FIX
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  3. FIX

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  4. Merge pull request c-proof#204 from jklymak/fix-read-the-docs 

    FIX
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  5. FIX

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  6. Merge pull request c-proof#205 from jklymak/fix-read-the-docs 

    FIX
    @jklymak
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  7. DOC: small changes to slocum

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  8. Merge pull request c-proof#206 from jklymak/doc-slocum-fixes 

    DOC: small changes to slocum
    @jklymak
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  9. DOC: small changes to slocum

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  10. Merge pull request c-proof#207 from jklymak/doc-slocum-fixes 

    DOC: small changes to slocum
    @jklymak
    jklymak authored Oct 29, 2024
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  11. DOC: small changes to slocum

    @jklymak
    jklymak committed Oct 29, 2024
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  12. Merge pull request c-proof#208 from jklymak/doc-slocum-fixes 

    DOC: small changes to slocum
    @jklymak
    jklymak authored Oct 29, 2024
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Commits on Nov 5, 2024

  1. Updates 

     * We do not want to ignore the first line of any data
 * Do not interpolate the data (get_sync -> get)
 * .gitignore: Ignore build directory
    @jr3cermak
    jr3cermak committed Nov 5, 2024
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Commits on Nov 8, 2024

  1. Updates 

     * Ignore build directory
    @jr3cermak
    jr3cermak committed Nov 8, 2024
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Commits on Nov 23, 2024

  1. Updates 

     * Add gitignore files and directories created by running pytest
 * Allow setting time and calendar units from yml configuration file
 * Fix to allow profile_time_start and profile_time_end to get time
   information by moving time_1970 to last variable processed in
   for loop
 * Emit warning for variables lacking data for gridding
 * Add resync_metadata_and_encoding to allow overriding of metadata
   from yml configuration file
 * Fix log message for raw_to_timeseries
 * Allow conversion of slocum latitude and longitude from NMEA to degrees
 * Emit log message when metadata is overridden from yml configuration file
 * Add utils function to determine pyglider version
 * Add utils function to determine netcdf C and python versions
 * Set units for profile_time in example-slocum/deploymentRealtime.yml to
   get proper units for profile_time
 * Remove history and netcdf attributes as they can now vary widely from
   static examples
    @jr3cermak
    jr3cermak committed Nov 23, 2024
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  2. Merge remote-tracking branch 'refs/remotes/origin/uwfardev' into uwfa… 

    …rdev
    @jr3cermak
    jr3cermak committed Nov 23, 2024
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