Dependency refresh and bumps (#334)

* Dependency refresh and bumps

* Limited python version to <3.11.
* poetry update on packages.

Noteable upgrades:
* `astropy` v4.3 -> v5.0.
* `mkdocs-material` v7.3.0 -> v8.2.4.

* poetry update 20230426

* Add python 3.10 to testing

* Updated pyarrow & removed python upper constraint

* Fixed one tools moc test

* Update astropy to v6

* adjust astropy version

* Fix Adam email syntax

* Fixed README syntax error

* Updated Emil affiliation

* Update mocpy version

* Update colorcet to remove annoying matplotlib errors

* Fix mocpy versioning

* More versioning

* Fix max_depth argument

* Fix get_cmap deprecation warning

* Fixed Ellipse angle warning

* Changes

* PEP8

* README typo fix

* Fix time comparison

* Add max_depth argument

* versioning

* Finally fixed mocpy version issues

* Try python 3.11

* Updated poetry.lock

* PEP8

* Revert to python<3.11

* Fixed links in source.md

* Fix typo in docstring

* Added return type to vasttools.utils.open_fits

* more version changes

* Move watch from mkdocstrings to native mkdocs

* PEP8

* Update file emoji key

* More version fiddling

* Commit poetry.lock

* Remove randomly added comma

* Remove hardcoded time_depth

* Remove lightgallery support

* Updated changelog

* More changelog updates

* Final dependency updates

* Updated bokeh plot size syntax

* Fix minor docstring formatting oversights

* PEP8

* Updated changelog

* fixed matplotlib figure typing handling

* Fixed typing annotation

* Just realised I had uncommitted changes!

---------

Co-authored-by: Dougal Dobie <[email protected]>
Co-authored-by: Dougal Dobie <[email protected]>

.github/workflows/pytest.yml

@@ -8,7 +8,7 @@ jobs:
     strategy:
       fail-fast: false
       matrix:
-        python_version: ['3.8', '3.9']
+        python_version: ['3.8', '3.9', '3.10']
 
     steps:
         - uses: actions/checkout@v4

CHANGELOG.md

@@ -8,19 +8,31 @@ The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/),
 
 #### Added
 
+- Support for Python 3.10 [#334](https://github.com/askap-vast/vast-tools/pull/334)
 - Add access to epoch 63 [#563](https://github.com/askap-vast/vast-tools/pull/563)
 
 #### Changed
 
+- Minor changes to docstring formatting throughout based on updated mkdocs versions [#334](https://github.com/askap-vast/vast-tools/pull/334)
+- Minor changes for matplotlib 3.7: add angle kwarg to Ellipse and change matplotlib.pyplot.cm.get_cmap to matplotlib.colormaps.get_cmap [#334](https://github.com/askap-vast/vast-tools/pull/334)
+- Refreshed dependencies - major changes are python 3.10, mkdocs (and related packages), astropy v5 and matplotlib v3.7 [#334](https://github.com/askap-vast/vast-tools/pull/334)
+- Update emoji names to reflect latest fontawesome naming scheme[#334](https://github.com/askap-vast/vast-tools/pull/334)
+- Fixed minor typos in docs and docstrings [#334](https://github.com/askap-vast/vast-tools/pull/334)
+- Updated old contact information [#334](https://github.com/askap-vast/vast-tools/pull/334)
 - Updated github actions to latest versions [#562](https://github.com/askap-vast/vast-tools/pull/562)
 - Updated 2023 workshop notebook - fixed Query options and general cleanup [#558](https://github.com/askap-vast/vast-tools/pull/558)
 
 #### Fixed
 
+- Directly compare stmoc times, avoiding conversion to JD, and replace equality requirement with `isclose` [#334](https://github.com/askap-vast/vast-tools/pull/334)
+
 #### Removed
 
+- Removed lightgallery functionality from docs [#334](https://github.com/askap-vast/vast-tools/pull/334)
+
 #### List of PRs
 
+- [#334](https://github.com/askap-vast/vast-tools/pull/334): fix, docs, feat: Dependency refresh including python 3.10 support and corresponding minor updates
 - [#563](https://github.com/askap-vast/vast-tools/pull/563): feat: Add access to epoch 63
 - [#562](https://github.com/askap-vast/vast-tools/pull/562): fix: Updated github actions to latest versions
 - [#558](https://github.com/askap-vast/vast-tools/pull/558): docs: Updated 2023 workshop notebook - fixed Query options and general cleanup

README.md

@@ -34,10 +34,10 @@ Take a look at the [example notebooks](https://github.com/askap-vast/vast-tools/
 ### Active
 
 * Adam Stewart – [Sydney Institute for Astronomy](https://sifa.sydney.edu.au/)
-* Dougal Dobie – [[Sydney Institute for Astronomy](https://sifa.sydney.edu.au/) and [OzGrav](https://www.ozgrav.org)
+* Dougal Dobie – [Sydney Institute for Astronomy](https://sifa.sydney.edu.au/) and [OzGrav](https://www.ozgrav.org)
 
 ### Former
-* Emil Lenc [CSIRO]
+* Emil Lenc [Australia Telescope National Facility](https://www.atnf.csiro.au/)
 * Andrew O'Brien – [Department of Physics, University of Wisconsin-Milwaukee](https://uwm.edu/physics/research/astronomy-gravitation-cosmology/)
 * Tara Murphy – [Sydney Institute for Astronomy](https://sifa.sydney.edu.au/)
 * David Kaplan – [Department of Physics, University of Wisconsin-Milwaukee](https://uwm.edu/physics/research/astronomy-gravitation-cosmology/)

docs/components/mocs.md

@@ -55,7 +55,7 @@ The following methods are available with the `VASTMOCS` class.
 
 #### load_pilot_tile_moc
 
-:fontawesome-regular-file-alt: [Code reference](../../reference/moc/#vasttools.moc.VASTMOCS.load_pilot_tile_moc).
+:fontawesome-regular-file-lines: [Code reference](../../reference/moc/#vasttools.moc.VASTMOCS.load_pilot_tile_moc).
 
 This loads the MOC of a single tile, returning a `mocpy.MOC` instance.
 
@@ -67,7 +67,7 @@ This loads the MOC of a single tile, returning a `mocpy.MOC` instance.
 
 #### load_pilot_field_moc
 
-:fontawesome-regular-file-alt: [Code reference](../../reference/moc/#vasttools.moc.VASTMOCS.load_pilot_field_moc).
+:fontawesome-regular-file-lines: [Code reference](../../reference/moc/#vasttools.moc.VASTMOCS.load_pilot_field_moc).
 
 This loads the MOC of a VAST pilot survey field, returning a `mocpy.MOC` instance.
 
@@ -79,7 +79,7 @@ This loads the MOC of a VAST pilot survey field, returning a `mocpy.MOC` instanc
 
 #### load_pilot_epoch_moc
 
-:fontawesome-regular-file-alt: [Code reference](../../reference/moc/#vasttools.moc.VASTMOCS.load_pilot_epoch_moc).
+:fontawesome-regular-file-lines: [Code reference](../../reference/moc/#vasttools.moc.VASTMOCS.load_pilot_epoch_moc).
 
 This loads the MOC of a VAST pilot survey epoch, returning a `mocpy.MOC` instance.
 Enter as string with no zero padding on the epoch.
@@ -92,7 +92,7 @@ Enter as string with no zero padding on the epoch.
 
 #### load_pilot_stmoc
 
-:fontawesome-regular-file-alt: [Code reference](../../reference/moc/#vasttools.moc.VASTMOCS.load_pilot_stmoc).
+:fontawesome-regular-file-lines: [Code reference](../../reference/moc/#vasttools.moc.VASTMOCS.load_pilot_stmoc).
 
 This loads the STMOC of all the VAST pilot observations, returning a `mocpy.MOC` instance.
 
@@ -104,7 +104,7 @@ This loads the STMOC of all the VAST pilot observations, returning a `mocpy.MOC`
 
 #### load_survey_footprint
 
-:fontawesome-regular-file-alt: [Code reference](../../reference/moc/#vasttools.moc.VASTMOCS.load_survey_footprint).
+:fontawesome-regular-file-lines: [Code reference](../../reference/moc/#vasttools.moc.VASTMOCS.load_survey_footprint).
 
 This loads a MOC of the footprint of either the pilot or full VAST survey.
 
@@ -117,7 +117,7 @@ This loads a MOC of the footprint of either the pilot or full VAST survey.
 
 #### query_vizier_vast_pilot
 
-:fontawesome-regular-file-alt: [Code reference](../../reference/moc/#vasttools.moc.VASTMOCS.query_vizier_vast_pilot).
+:fontawesome-regular-file-lines: [Code reference](../../reference/moc/#vasttools.moc.VASTMOCS.query_vizier_vast_pilot).
 
 This searches the provided Vizier table for sources that are in the VAST pilot survey epoch 1 footprint, returning a `astropy.table.Table` instance.
 

docs/components/pipeline.md

@@ -47,7 +47,7 @@ The following methods are available with the `Pipeline` instance.
 
 #### list_images
 
-:fontawesome-regular-file-alt: [Code reference](../../reference/pipeline/#vasttools.pipeline.Pipeline.list_images).
+:fontawesome-regular-file-lines: [Code reference](../../reference/pipeline/#vasttools.pipeline.Pipeline.list_images).
 
 Provides a list of all the images that have been processed in the pipeline.
 
@@ -67,7 +67,7 @@ Provides a list of all the images that have been processed in the pipeline.
 
 #### list_piperuns
 
-:fontawesome-regular-file-alt: [Code reference](../../reference/pipeline/#vasttools.pipeline.Pipeline.list_piperuns).
+:fontawesome-regular-file-lines: [Code reference](../../reference/pipeline/#vasttools.pipeline.Pipeline.list_piperuns).
 
 Provides a list of all the pipeline runs that have been set up in the pipeline.
 
@@ -88,7 +88,7 @@ Provides a list of all the pipeline runs that have been set up in the pipeline.
 
 #### load_run
 
-:fontawesome-regular-file-alt: [Code reference](../../reference/pipeline/#vasttools.pipeline.Pipeline.load_run).
+:fontawesome-regular-file-lines: [Code reference](../../reference/pipeline/#vasttools.pipeline.Pipeline.load_run).
 
 Loads the pipeline run requested returning a `vasttools.pipeline.PipeAnalysis` instance (see sections below).
 
@@ -100,7 +100,7 @@ Loads the pipeline run requested returning a `vasttools.pipeline.PipeAnalysis` i
 
 #### load_runs
 
-:fontawesome-regular-file-alt: [Code reference](../../reference/pipeline/#vasttools.pipeline.Pipeline.load_runs).
+:fontawesome-regular-file-lines: [Code reference](../../reference/pipeline/#vasttools.pipeline.Pipeline.load_runs).
 
 Loads multiple pipeline runs that are requested and merges them to return a single `vasttools.pipeline.PipeAnalysis` instance (see sections below).
 
@@ -122,7 +122,7 @@ The sections below detail what data and methods are available.
 
 ### Accessing PipeAnalysis Run Data
 
-:fontawesome-regular-file-alt: [Code reference](../../reference/pipeline/#vasttools.pipeline.PipeAnalysis).
+:fontawesome-regular-file-lines: [Code reference](../../reference/pipeline/#vasttools.pipeline.PipeAnalysis).
 
 The run data is stored as attributes to the `PipeAnalysis` object, which are all shown in the table below.
 This means that to access any of the pieces of pipeline run data, for example `sources`, the command would be:
@@ -174,7 +174,7 @@ The following methods are available to the `PipeAnalysis` instance.
 
 #### check_for_planets
 
-:fontawesome-regular-file-alt: [Code reference](../../reference/pipeline/#vasttools.pipeline.PipeRun.check_for_planets).
+:fontawesome-regular-file-lines: [Code reference](../../reference/pipeline/#vasttools.pipeline.PipeRun.check_for_planets).
 
 Checks to see if any of the planets, including Pluto, the Sun and the Moon, are observable at any time in the pipeline run.
 A pandas dataframe will be returned containing the positions of found objects. 
@@ -197,7 +197,7 @@ The columns of the returned dataframe are:
 
 #### combine_with_run
 
-:fontawesome-regular-file-alt: [Code reference](../../reference/pipeline/#vasttools.pipeline.PipeRun.combine_with_run).
+:fontawesome-regular-file-lines: [Code reference](../../reference/pipeline/#vasttools.pipeline.PipeRun.combine_with_run).
 
 Combines the current run with another `PipeAnalysis` object that has been loaded, i.e. a second pipeline run.
 It returns a new `PipeAnalysis` object with the two runs combined.
@@ -214,7 +214,7 @@ It returns a new `PipeAnalysis` object with the two runs combined.
 
 #### create_moc
 
-:fontawesome-regular-file-alt: [Code reference](../../reference/pipeline/#vasttools.pipeline.PipeRun.create_moc).
+:fontawesome-regular-file-lines: [Code reference](../../reference/pipeline/#vasttools.pipeline.PipeRun.create_moc).
 
 This creates a Multi-Order Coverage map for the area covered by the pipeline run. 
 
@@ -228,7 +228,7 @@ This creates a Multi-Order Coverage map for the area covered by the pipeline run
 
 #### filter_by_moc
 
-:fontawesome-regular-file-alt: [Code reference](../../reference/pipeline/#vasttools.pipeline.PipeRun.filter_by_moc).
+:fontawesome-regular-file-lines: [Code reference](../../reference/pipeline/#vasttools.pipeline.PipeRun.filter_by_moc).
 
 Returns a new `PipeAnalysis` instance that has had all data filtered to only include data of sources that are within a supplied MOC.
 
@@ -240,7 +240,7 @@ Returns a new `PipeAnalysis` instance that has had all data filtered to only inc
 
 #### get_source
 
-:fontawesome-regular-file-alt: [Code reference](../../reference/pipeline/#vasttools.pipeline.PipeRun.get_source).
+:fontawesome-regular-file-lines: [Code reference](../../reference/pipeline/#vasttools.pipeline.PipeRun.get_source).
 
 Fetches a specific source from the pipeline run, and returns a `vasttools.source.Source` instance.
 The source is selected by using the ID value.
@@ -257,7 +257,7 @@ The source is selected by using the ID value.
 
 #### get_sources_skycoord
 
-:fontawesome-regular-file-alt: [Code reference](../../reference/pipeline/#vasttools.pipeline.PipeRun.get_sources_skycoord).
+:fontawesome-regular-file-lines: [Code reference](../../reference/pipeline/#vasttools.pipeline.PipeRun.get_sources_skycoord).
 
 A convenience function to generate a `SkyCoord` object of all the sources in the `PipeAnalysis.sources` attribute.
 Returns a `astropy.coordines.SkyCoord` instance.
@@ -273,7 +273,7 @@ Returns a `astropy.coordines.SkyCoord` instance.
 
 #### load_two_epoch_metrics
 
-:fontawesome-regular-file-alt: [Code reference](../../reference/pipeline/#vasttools.pipeline.PipeRun.load_two_epoch_metrics).
+:fontawesome-regular-file-lines: [Code reference](../../reference/pipeline/#vasttools.pipeline.PipeRun.load_two_epoch_metrics).
 
 By default the raw two-epoch metrics produced by the pipeline are not loaded.
 This method loads the two-epoch metrics, stored by the pipeline in `measurement_pairs.parquet` (or `measurement_pairs.arrow`) and saves them as an attribute to the `PipeAnalysis` object: `PipeAnalysis.measurement_pairs_df`.
@@ -300,7 +300,7 @@ This is stored as the attribute `PipeAnalysis.pairs_df`.
 
 #### recalc_measurement_pairs_df
 
-:fontawesome-regular-file-alt: [Code reference](../../reference/pipeline/#vasttools.pipeline.PipeAnalysis.recalc_measurement_pairs_df).
+:fontawesome-regular-file-lines: [Code reference](../../reference/pipeline/#vasttools.pipeline.PipeAnalysis.recalc_measurement_pairs_df).
 
 !!! warning "Warning: Run Time & Memory"
     Beware that for large pipeline runs the recalculation can take some time to complete and use up considerable memory.
@@ -319,7 +319,7 @@ For example, some measurements could have been removed or the fluxes could have
 
 #### recalc_sources_df
 
-:fontawesome-regular-file-alt: [Code reference](../../reference/pipeline/#vasttools.pipeline.PipeAnalysis.recalc_sources_df).
+:fontawesome-regular-file-lines: [Code reference](../../reference/pipeline/#vasttools.pipeline.PipeAnalysis.recalc_sources_df).
 
 !!! warning "Warning: Run Time & Memory"
     Beware that for large pipeline runs the recalculation can take some time to complete and use up considerable memory.
@@ -370,7 +370,7 @@ The following methods are designed to perform common transient search analyses a
 
 #### eta_v_diagnostic_plot
 
-:fontawesome-regular-file-alt: [Code reference](../../reference/pipeline/#vasttools.pipeline.PipeAnalysis.eta_v_diagnostic_plot).
+:fontawesome-regular-file-lines: [Code reference](../../reference/pipeline/#vasttools.pipeline.PipeAnalysis.eta_v_diagnostic_plot).
 
 Produces a diagnostic plot using the η and V metrics as described in [Rowlinson et al., 2019](https://ui.adsabs.harvard.edu/abs/2019A%26C....27..111R/abstract).
 Returns a `matplotlib.pyplot.figure` instance.
@@ -385,7 +385,7 @@ Returns a `matplotlib.pyplot.figure` instance.
 
 #### plot_two_epoch_pairs
 
-:fontawesome-regular-file-alt: [Code reference](../../reference/pipeline/#vasttools.pipeline.PipeAnalysis.plot_two_epoch_pairs).
+:fontawesome-regular-file-lines: [Code reference](../../reference/pipeline/#vasttools.pipeline.PipeAnalysis.plot_two_epoch_pairs).
 
 Produce a two-epoch metric plot of the `m` and `vs` values of the requested pair ID (i.e. the pair of images).
 The pair ID can be found in the `pairs_df` attribute after [`load_two_epoch_metrics()`](#load_two_epoch_metrics) has been used.
@@ -420,7 +420,7 @@ where as style `b` follows the style found in [Radcliffe et al., 2019](https://u
 
 #### run_eta_v_analysis
 
-:fontawesome-regular-file-alt: [Code reference](../../reference/pipeline/#vasttools.pipeline.PipeAnalysis.run_eta_v_analysis).
+:fontawesome-regular-file-lines: [Code reference](../../reference/pipeline/#vasttools.pipeline.PipeAnalysis.run_eta_v_analysis).
 
 Method to perform the η-V transient search method as described in [Rowlinson et al., 2019](https://ui.adsabs.harvard.edu/abs/2019A%26C....27..111R/abstract), to the sigma level provided for each metric.
 It uses the η and V metrics defined in the `sources` dataframe.
@@ -481,7 +481,7 @@ The candidates plot can either be a `matplotlib.pyplot.figure` or `bokeh.layouts
 
 #### run_two_epoch_analysis
 
-:fontawesome-regular-file-alt: [Code reference](../../reference/pipeline/#vasttools.pipeline.PipeAnalysis.run_two_epoch_analysis).
+:fontawesome-regular-file-lines: [Code reference](../../reference/pipeline/#vasttools.pipeline.PipeAnalysis.run_two_epoch_analysis).
 
 Method to perform the two epoch analysis as detailed in [Mooley et al., 2016](https://ui.adsabs.harvard.edu/abs/2016ApJ...818..105M/abstract) to the provided `m` and `vs` threshold values.
 The entire `measurement_pairs_df` is analysed for any pair that exceed the two provided thresholds.

docs/components/query.md

@@ -41,7 +41,7 @@ In full, the `Query` component as the ability to:
 !!! info "Info: Query Notebook Example"
      An example notebook of using the Query component can be found in the example notebooks section [here](../../notebook-examples/source-search-example/).
 
-:fontawesome-regular-file-alt: [Code reference](../../reference/query/#vasttools.query.Query).
+:fontawesome-regular-file-lines: [Code reference](../../reference/query/#vasttools.query.Query).
 
 A `Query` instance can be imported from `vasttools.query`: