diff --git a/.github/workflows/pytest.yml b/.github/workflows/pytest.yml
index 03db1b8b..6826a91d 100644
--- a/.github/workflows/pytest.yml
+++ b/.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
diff --git a/CHANGELOG.md b/CHANGELOG.md
index 0723b276..dfe43988 100644
--- a/CHANGELOG.md
+++ b/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
diff --git a/README.md b/README.md
index 60fc9133..18b2206d 100644
--- a/README.md
+++ b/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/)
diff --git a/docs/components/mocs.md b/docs/components/mocs.md
index 5423a8f8..bf28a9e0 100644
--- a/docs/components/mocs.md
+++ b/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.
diff --git a/docs/components/pipeline.md b/docs/components/pipeline.md
index 6b51305a..6670f325 100644
--- a/docs/components/pipeline.md
+++ b/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.
diff --git a/docs/components/query.md b/docs/components/query.md
index c6afcb3d..6f42c912 100644
--- a/docs/components/query.md
+++ b/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`:
diff --git a/docs/components/source.md b/docs/components/source.md
index 68f230c4..0e20ec75 100644
--- a/docs/components/source.md
+++ b/docs/components/source.md
@@ -40,7 +40,7 @@ If a `Source` instance is required to be initialised then the first step is to i
A number of arguments are required to initialise a `Source` instance.
Those that are required are described below, along with an example.
-!!! info ":fontawesome-regular-file-alt: Code Reference"
+!!! info ":fontawesome-regular-file-lines: Code Reference"
See the [Code reference](../../reference/source/#vasttools.source.Source.__init__) section for all the initialisation options.
!!! warning "Warning: `Query` biased"
@@ -131,7 +131,7 @@ The standard VAST Pilot Survey data release structure is assumed (refer to [Conf
A `Source` instance contains several useful attributes.
-!!! info ":fontawesome-regular-file-alt: Code Reference"
+!!! info ":fontawesome-regular-file-lines: Code Reference"
See the [Code reference](../../reference/source/#vasttools.source.Source) section for all the `Source` attributes.
The two most commonly accessed attributes are:
@@ -181,7 +181,7 @@ The following methods are available with the `Source` instance.
#### calc_eta_and_v_metrics
-:fontawesome-regular-file-alt: [Code reference](../../reference/source/#vasttools.source.Source.calc_eta_and_v_metrics).
+:fontawesome-regular-file-lines: [Code reference](../../reference/source/#vasttools.source.Source.calc_eta_and_v_metrics).
Calculates the `η` and `V` variability metrics.
By default the peak flux is used.
@@ -193,7 +193,7 @@ By default the peak flux is used.
#### calc_eta_metric
-:fontawesome-regular-file-alt: [Code reference](../../reference/source/#vasttools.source.Source.calc_eta_metric).
+:fontawesome-regular-file-lines: [Code reference](../../reference/source/#vasttools.source.Source.calc_eta_metric).
Calculates the `η` variability metric.
By default the peak flux is used.
@@ -205,7 +205,7 @@ By default the peak flux is used.
#### calc_v_metric
-:fontawesome-regular-file-alt: [Code reference](../../reference/source/#vasttools.source.Source.calc_v_metric).
+:fontawesome-regular-file-lines: [Code reference](../../reference/source/#vasttools.source.Source.calc_v_metric).
Calculates the `V` variability metric.
By default the peak flux is used.
@@ -217,7 +217,7 @@ By default the peak flux is used.
#### casda_search
-:fontawesome-regular-file-alt: [Code reference](../../reference/source/#vasttools.source.Source.casda_search).
+:fontawesome-regular-file-lines: [Code reference](../../reference/source/#vasttools.source.Source.casda_search).
Uses the [`astoquery CASDA Queries`](https://astroquery.readthedocs.io/en/latest/casda/casda.html){:target="_blank"} service to perform a search of the
[CSIRO ASKAP Science Data Archive (CASDA)](https://research.csiro.au/casda/){:target="_blank"} for all ASKAP observations that contain the respective source.
@@ -232,7 +232,7 @@ Results are returned as an [`astropy table`](https://docs.astropy.org/en/stable/
#### get_cutout_data
-:fontawesome-regular-file-alt: [Code reference](../../reference/source/#vasttools.source.Source.get_cutout_data).
+:fontawesome-regular-file-lines: [Code reference](../../reference/source/#vasttools.source.Source.get_cutout_data).
This method fetches the cutout data that is required to generate the postage stamps and additional overlays.
The cutout data is stored in a dataframe as the attribute `Source.cutout_df`.
@@ -248,7 +248,7 @@ The cutout data is stored in a dataframe as the attribute `Source.cutout_df`.
#### make_png
-:fontawesome-regular-file-alt: [Code reference](../../reference/source/#vasttools.source.Source.make_png).
+:fontawesome-regular-file-lines: [Code reference](../../reference/source/#vasttools.source.Source.make_png).
The main method that generates all the PNG images that is called by other methods.
Note that this method can only produce a single epoch at a time, and the required argument is the index of the observation to plot.
@@ -289,7 +289,7 @@ By default the axis labels will measure the offset from the central coordinate.
#### ned_search
-:fontawesome-regular-file-alt: [Code reference](../../reference/source/#vasttools.source.Source.ned_search).
+:fontawesome-regular-file-lines: [Code reference](../../reference/source/#vasttools.source.Source.ned_search).
Uses the [`astoquery NED Queries`](https://astroquery.readthedocs.io/en/latest/ned/ned.html){:target="_blank"} service to perform a search of the
[NASA/IPAC Extragalactic Database (NED)](https://ned.ipac.caltech.edu){:target="_blank"} for possible counterparts to the source.
@@ -304,7 +304,7 @@ Results are returned as an [`astropy table`](https://docs.astropy.org/en/stable/
#### plot_lightcurve
-:fontawesome-regular-file-alt: [Code reference](../../reference/source/#vasttools.source.Source.plot_lightcurve).
+:fontawesome-regular-file-lines: [Code reference](../../reference/source/#vasttools.source.Source.plot_lightcurve).
A method that returns a plot of the source lightcurve.
The result is returned a [`matplotlib.pyplot.figure`](https://matplotlib.org/stable/api/_as_gen/matplotlib.pyplot.figure.html){:target="_blank"} instance.
@@ -321,16 +321,16 @@ There are a wide variety of options that can style the output plot, please refer
#### save_all_ann
-:fontawesome-regular-file-alt: [Code reference](../../reference/source/#vasttools.source.Source.save_all_ann).
+:fontawesome-regular-file-lines: [Code reference](../../reference/source/#vasttools.source.Source.save_all_ann).
A method to save the [kvis annotation files](https://www.atnf.csiro.au/computing/software/karma/user-manual/node17.html){:target="_blank"} for all epochs.
-Refer to the method [`write_ann`](#write-ann) for saving the annotation file for an individual epoch.
+Refer to the method [`write_ann`](#write_ann) for saving the annotation file for an individual epoch.
The target source and all surrounding sources are included.
The files will be saved to the directory specified by the argument `outdir` in the instancing of the `Source`.
If this was not provided the default location is the current directory.
!!! note "Note: Change Cutout Size"
- To change the size of the cutout, re-fetch the cutout data using the [`get_cutout_data`](#get-cutout-data) method.
+ To change the size of the cutout, re-fetch the cutout data using the [`get_cutout_data`](#get_cutout_data) method.
!!! example
```python
@@ -339,10 +339,10 @@ If this was not provided the default location is the current directory.
#### save_all_fits_cutouts
-:fontawesome-regular-file-alt: [Code reference](../../reference/source/#vasttools.source.Source.save_all_fits_cutouts).
+:fontawesome-regular-file-lines: [Code reference](../../reference/source/#vasttools.source.Source.save_all_fits_cutouts).
A method to save the cutouts (or postage stamps) of each epoch as individual FITS files.
-Refer to the method [`save_fits_cutout`](#save-fits-cutout) for saving the FITS of an individual epoch.
+Refer to the method [`save_fits_cutout`](#save_fits_cutout) for saving the FITS of an individual epoch.
The FITS files will be saved to the directory specified by the argument `outdir` in the instancing of the `Source`.
If this was not provided the default location is the current directory.
@@ -361,10 +361,10 @@ If this was not provided the default location is the current directory.
#### save_all_png_cutouts
-:fontawesome-regular-file-alt: [Code reference](../../reference/source/#vasttools.source.Source.save_all_png_cutouts).
+:fontawesome-regular-file-lines: [Code reference](../../reference/source/#vasttools.source.Source.save_all_png_cutouts).
A method to save the cutouts (or postage stamps) of each epoch as individual png files.
-Refer to the method [`save_png_cutout`](#save-png-cutout) for saving the png for an individual epoch.
+Refer to the method [`save_png_cutout`](#save_png_cutout) for saving the png for an individual epoch.
The png files will be saved to the directory specified by the argument `outdir` in the instancing of the `Source`.
If this was not provided the default location is the current directory.
@@ -377,8 +377,8 @@ If this was not provided the default location is the current directory.
```
!!! warning
- This is not an analogous method to [`show_all_png_cutouts`](#show-all-png-cutouts).
- The method will produce the result from [`save_png_cutout`](#save-png-cutout) but for each epoch.
+ This is not an analogous method to [`show_all_png_cutouts`](#show_all_png_cutouts).
+ The method will produce the result from [`save_png_cutout`](#save_png_cutout) but for each epoch.
The result from `show_all_png_cutouts` must be saved using the returned figure.
!!! example
@@ -388,16 +388,16 @@ If this was not provided the default location is the current directory.
#### save_all_reg
-:fontawesome-regular-file-alt: [Code reference](../../reference/source/#vasttools.source.Source.save_all_reg).
+:fontawesome-regular-file-lines: [Code reference](../../reference/source/#vasttools.source.Source.save_all_reg).
A method to save the [DS9 region files](https://ds9.si.edu/doc/ref/region.html){:target="_blank"} for all epochs.
-Refer to the method [`write_reg`](#write-reg) for saving the region file for an individual epoch.
+Refer to the method [`write_reg`](#write_reg) for saving the region file for an individual epoch.
The target source and all surrounding sources are included.
The files will be saved to the directory specified by the argument `outdir` in the instancing of the `Source`.
If this was not provided the default location is the current directory.
!!! note "Note: Change Cutout Size"
- To change the size of the cutout, re-fetch the cutout data using the [`get_cutout_data`](#get-cutout-data) method.
+ To change the size of the cutout, re-fetch the cutout data using the [`get_cutout_data`](#get_cutout_data) method.
!!! example
```python
@@ -406,7 +406,7 @@ If this was not provided the default location is the current directory.
#### save_fits_cutout
-:fontawesome-regular-file-alt: [Code reference](../../reference/source/#vasttools.source.Source.save_fits_cutout).
+:fontawesome-regular-file-lines: [Code reference](../../reference/source/#vasttools.source.Source.save_fits_cutout).
A method to save the cutout (or postage stamp) of a single observation in the FITS format.
The required argument is the zero-based index of the observation to be saved.
@@ -430,7 +430,7 @@ If this was not provided the default location is the current directory.
#### save_png_cutout
-:fontawesome-regular-file-alt: [Code reference](../../reference/source/#vasttools.source.Source.save_png_cutout).
+:fontawesome-regular-file-lines: [Code reference](../../reference/source/#vasttools.source.Source.save_png_cutout).
A method to save the cutout (or postage stamp) of a single observation as a png image.
The required argument is the zero-based index of the epoch to be saved.
@@ -457,7 +457,7 @@ If this was not provided the default location is the current directory.
#### show_all_png_cutouts
-:fontawesome-regular-file-alt: [Code reference](../../reference/source/#vasttools.source.Source.show_all_png_cutouts).
+:fontawesome-regular-file-lines: [Code reference](../../reference/source/#vasttools.source.Source.show_all_png_cutouts).
A method to produce a single image containing all the cutouts of the source, i.e. those from each epoch, displayed.
Refer to the code reference for all other available options.
@@ -485,7 +485,7 @@ The result is returned a [`matplotlib.pyplot.figure`](https://matplotlib.org/sta
#### show_png_cutout
-:fontawesome-regular-file-alt: [Code reference](../../reference/source/#vasttools.source.Source.show_png_cutout).
+:fontawesome-regular-file-lines: [Code reference](../../reference/source/#vasttools.source.Source.show_png_cutout).
A method to produce the cutout (or postage stamp) of a single observation as a png image.
The required argument is the zero-based index of the observation to be saved.
@@ -511,7 +511,7 @@ The result is returned a [`matplotlib.pyplot.figure`](https://matplotlib.org/sta
#### simbad_search
-:fontawesome-regular-file-alt: [Code reference](../../reference/source/#vasttools.source.Source.simbad_search).
+:fontawesome-regular-file-lines: [Code reference](../../reference/source/#vasttools.source.Source.simbad_search).
Uses the [`astoquery SIMBAD Queries`](https://astroquery.readthedocs.io/en/latest/simbad/simbad.html){:target="_blank"} service to perform a search of
[SIMBD](https://simbad.u-strasbg.fr/simbad/){:target="_blank"} for possible counterparts to the source.
@@ -526,7 +526,7 @@ Results are returned as an [`astropy table`](https://docs.astropy.org/en/stable/
#### skyview_contour_plot
-:fontawesome-regular-file-alt: [Code reference](../../reference/source/#vasttools.source.Source.skyview_contour_plot).
+:fontawesome-regular-file-lines: [Code reference](../../reference/source/#vasttools.source.Source.skyview_contour_plot).
Uses the [`astroquery Skyview Queries`](https://astroquery.readthedocs.io/en/latest/skyview/skyview.html){:target="_blank"} service to download and display a cutout from an available external survey
and overlay contours of the source from the selected observation.
@@ -555,7 +555,7 @@ The result is returned a [`matplotlib.pyplot.figure`](https://matplotlib.org/sta
#### write_ann
-:fontawesome-regular-file-alt: [Code reference](../../reference/source/#vasttools.source.Source.write_ann).
+:fontawesome-regular-file-lines: [Code reference](../../reference/source/#vasttools.source.Source.write_ann).
Saves the kvis annotation file equal to the generated cutout size for the provided observation.
The target source and all surrounding sources are included.
@@ -564,7 +564,7 @@ The file will be saved to the directory specified by the argument `outdir` in th
If this was not provided the default location is the current directory.
!!! note "Note: Change Cutout Size"
- To change the size of the cutout, re-fetch the cutout data using the [`get_cutout_data`](#get-cutout-data) method.
+ To change the size of the cutout, re-fetch the cutout data using the [`get_cutout_data`](#get_cutout_data) method.
!!! example
Save the annotation file for the first observation.
@@ -574,7 +574,7 @@ If this was not provided the default location is the current directory.
#### write_measurements
-:fontawesome-regular-file-alt: [Code reference](../../reference/source/#vasttools.source.Source.write_measurements).
+:fontawesome-regular-file-lines: [Code reference](../../reference/source/#vasttools.source.Source.write_measurements).
A convenience method to save the measurements dataframe (i.e. `Source.measurements`) to a file.
The file will be saved to the directory specified by the argument `outdir` in the instancing of the `Source`.
@@ -587,7 +587,7 @@ If this was not provided the default location is the current directory.
#### write_reg
-:fontawesome-regular-file-alt: [Code reference](../../reference/source/#vasttools.source.Source.write_reg).
+:fontawesome-regular-file-lines: [Code reference](../../reference/source/#vasttools.source.Source.write_reg).
Saves the ds9 region file of the generated cutout size for the provided observation.
The target source and all surrounding sources are included.
@@ -596,7 +596,7 @@ The file will be saved to the directory specified by the argument `outdir` in th
If this was not provided the default location is the current directory.
!!! note "Note: Change Cutout Size"
- To change the size of the cutout, re-fetch the cutout data using the [`get_cutout_data`](#get-cutout-data) method.
+ To change the size of the cutout, re-fetch the cutout data using the [`get_cutout_data`](#get_cutout_data) method.
!!! example
Save the region file for the first observation.
diff --git a/docs/components/survey.md b/docs/components/survey.md
index c4ccf4b0..b31ee2d6 100644
--- a/docs/components/survey.md
+++ b/docs/components/survey.md
@@ -13,13 +13,13 @@ The `Survey` component also contains two classes `Fields` and `Image` that may b
## Using the Survey Component
-:fontawesome-regular-file-alt: [Code reference](../../reference/survey).
+:fontawesome-regular-file-lines: [Code reference](../../reference/survey).
### Survey Component Functions
#### get_askap_observing_location
-:fontawesome-regular-file-alt: [Code reference](../../reference/survey/#vasttools.survey.get_askap_observing_location).
+:fontawesome-regular-file-lines: [Code reference](../../reference/survey/#vasttools.survey.get_askap_observing_location).
This function returns the location of the ASKAP telescope in the form of an [astropy EarthLocation instance](https://docs.astropy.org/en/stable/api/astropy.coordinates.EarthLocation.html){:target="_blank"}.
There are no arguments available to the function.
@@ -37,7 +37,7 @@ The values returned are the longitude, latitude and height.
#### get_fields_per_epoch_info
-:fontawesome-regular-file-alt: [Code reference](../../reference/survey/#vasttools.survey.get_fields_per_epoch_info).
+:fontawesome-regular-file-lines: [Code reference](../../reference/survey/#vasttools.survey.get_fields_per_epoch_info).
This function returns a pandas dataframe containing the field that are present in each epoch along with the SBID value and the date of the observation.
There are no arguments available to the function.
@@ -75,7 +75,7 @@ There are no arguments available to the function.
#### get_supported_epochs
-:fontawesome-regular-file-alt: [Code reference](../../reference/survey/#vasttools.survey.get_supported_epochs).
+:fontawesome-regular-file-lines: [Code reference](../../reference/survey/#vasttools.survey.get_supported_epochs).
Returns a list of the currently supported VAST Pilot Survey epochs.
@@ -92,7 +92,7 @@ Returns a list of the currently supported VAST Pilot Survey epochs.
#### load_field_centres
-:fontawesome-regular-file-alt: [Code reference](../../reference/survey/#vasttools.survey.load_field_centres).
+:fontawesome-regular-file-lines: [Code reference](../../reference/survey/#vasttools.survey.load_field_centres).
Returns a pandas dataframe containing three columns:
@@ -120,7 +120,7 @@ Returns a pandas dataframe containing three columns:
| 1015 | RACS_2359-43A | 0.00902694 | -43.8906 |
#### load_fields_skycoords
-:fontawesome-regular-file-alt: [Code reference](../../reference/survey/#vasttools.survey.load_fields_skycoords).
+:fontawesome-regular-file-lines: [Code reference](../../reference/survey/#vasttools.survey.load_fields_skycoords).
Ths function allows the user to load `SkyCoord` objects for all beam centres for a given epoch.
@@ -133,7 +133,7 @@ Ths function allows the user to load `SkyCoord` objects for all beam centres for
#### load_fields_file
-:fontawesome-regular-file-alt: [Code reference](../../reference/survey/#vasttools.survey.load_fields_file).
+:fontawesome-regular-file-lines: [Code reference](../../reference/survey/#vasttools.survey.load_fields_file).
This function allows the user to load the packaged field information file of the requested epoch as a pandas dataframe.
The included columns are:
@@ -171,7 +171,7 @@ The included columns are:
The `Fields` class is not intended for custom user usage and is designed to help internal processes.
However it is detailed here as it may prove useful in some situations and during development.
-:fontawesome-regular-file-alt: [Code reference](../../reference/survey/#vasttools.survey.Fields).
+:fontawesome-regular-file-lines: [Code reference](../../reference/survey/#vasttools.survey.Fields).
The `Fields` class is designed to act as a representation of the fields contained in an epoch.
It is primarily used by the `Query` component to perform the act of finding matches to provided sky coordinates.
@@ -179,7 +179,7 @@ The class holds details of the fields at the individual beam level rather than t
#### Initialising a Fields Instance
-:fontawesome-regular-file-alt: [Code reference](../../reference/survey/#vasttools.survey.Fields.__init__).
+:fontawesome-regular-file-lines: [Code reference](../../reference/survey/#vasttools.survey.Fields.__init__).
A `Fields` instance is initialised by declaring the epoch that is wanted to be represented.
This is demonstrated below.
@@ -194,7 +194,7 @@ This is demonstrated below.
#### Fields Attributes
-:fontawesome-regular-file-alt: [Code reference](../../reference/survey/#vasttools.survey.Fields)
+:fontawesome-regular-file-lines: [Code reference](../../reference/survey/#vasttools.survey.Fields)
The following attributes are available on a `Fields` instance.
@@ -251,13 +251,13 @@ An astropy [`SkyCoord`](https://docs.astropy.org/en/stable/api/astropy.coordinat
The `Image` class is not intended for custom user usage and is designed to help internal processes.
However it is detailed here as it may prove useful in some situations and during development.
-:fontawesome-regular-file-alt: [Code reference](../../reference/survey/#vasttools.survey.Image).
+:fontawesome-regular-file-lines: [Code reference](../../reference/survey/#vasttools.survey.Image).
The `Image` class provides a template of representing an individual ASKAP image, allowing for easy access to properties and common tasks.
#### Initialising an Image Instance
-:fontawesome-regular-file-alt: [Code reference](../../reference/survey/#vasttools.survey.Image.__init__).
+:fontawesome-regular-file-lines: [Code reference](../../reference/survey/#vasttools.survey.Image.__init__).
!!! warning "Warning: Pilot Survey Assumption"
By default the class was written to load images from the VAST Pilot Survey.
diff --git a/docs/components/tools.md b/docs/components/tools.md
index a07acfd0..8bf9ca32 100644
--- a/docs/components/tools.md
+++ b/docs/components/tools.md
@@ -8,12 +8,12 @@ The `Tools` sub-package is a mishmash of useful VAST-related functions that do n
## Using the Tools Component
-:fontawesome-regular-file-alt: [Code reference](../../reference/tools).
+:fontawesome-regular-file-lines: [Code reference](../../reference/tools).
### Skymaps and MOCs
#### skymap2moc
-:fontawesome-regular-file-alt: [Code reference](../../reference/tools/#vasttools.tools.skymap2moc).
+:fontawesome-regular-file-lines: [Code reference](../../reference/tools/#vasttools.tools.skymap2moc).
This function returns a MOC of the credible level of a provided skymap.
The arguments to this function are the path to the skymap file and the requested credible region.
@@ -26,7 +26,7 @@ The arguments to this function are the path to the skymap file and the requested
```
#### find_in_moc
-:fontawesome-regular-file-alt: [Code reference](../../reference/tools/#vasttools.tools.find_in_moc).
+:fontawesome-regular-file-lines: [Code reference](../../reference/tools/#vasttools.tools.find_in_moc).
This function returns the indices of sources that are contained within a given MOC, so that source catalogues can be filtered by sky region.
The arguments to this function are the MOC, the source DataFrame and an optional bool flagging whether the source dataframe is from the pipeline.
@@ -44,7 +44,7 @@ The value returned is a numpy array.
```
#### add_credible_levels
-:fontawesome-regular-file-alt: [Code reference](../../reference/tools/#vasttools.tools.add_credible_levels).
+:fontawesome-regular-file-lines: [Code reference](../../reference/tools/#vasttools.tools.add_credible_levels).
This function calculates the smallest credible region a source is contained in and adds it as a column, named `credible_level`, to the source dataframe in-place.
The arguments to this function are the path to the skymap file, the source DataFrame and an optional bool flagging whether the dataframe is from the pipeline.
@@ -67,7 +67,7 @@ The arguments to this function are the path to the skymap file, the source DataF
See the [Data Access](../../getting_started/configuration/#data-access) page for details.
#### create_fields_metadata
-:fontawesome-regular-file-alt: [Code reference](../../reference/tools/#vasttools.tools.create_fields_csv).
+:fontawesome-regular-file-lines: [Code reference](../../reference/tools/#vasttools.tools.create_fields_csv).
This function creates a fields csv file and a `SkyCoord` pickle for a given epoch using data from the [`ASKAP_SURVEYS`](https://bitbucket.csiro.au/projects/ASKAP_SURVEYS/repos/vast/browse){:target="_blank"} repository, which must be downloaded separately.
The arguments to this function are the epoch, the path to the repository and the path to the output directory, which defaults to the current directory.
@@ -80,7 +80,7 @@ The arguments to this function are the epoch, the path to the repository and the
```
#### add_obs_date
-:fontawesome-regular-file-alt: [Code reference](../../reference/tools/#vasttools.tools.add_obs_date).
+:fontawesome-regular-file-lines: [Code reference](../../reference/tools/#vasttools.tools.add_obs_date).
This function adds datetime data to all fits files in a given epoch.
The arguments to this function are the epoch, the image directory and the path to the epoch directory. If the path to the epoch directory is not provided it is generated from the `VAST_DATA_DIR` environment variable and the requested epoch.
@@ -93,7 +93,7 @@ The arguments to this function are the epoch, the image directory and the path t
```
#### gen_mocs_image
-:fontawesome-regular-file-alt: [Code reference](../../reference/tools/#vasttools.tools.gen_mocs_image).
+:fontawesome-regular-file-lines: [Code reference](../../reference/tools/#vasttools.tools.gen_mocs_image).
This function creates a MOC and STMOC from a single fits image. It is unlikely that users would ever have to call this directly, and it should instead be called as part of [`gen_mocs_epoch`](./gen_mocs_epoch).
The arguments to this function are the path to the fits file, whether to write the MOC/STMOC to file or simply return them, and the directory to write them to.
@@ -106,7 +106,7 @@ The arguments to this function are the path to the fits file, whether to write t
```
#### gen_mocs_epoch
-:fontawesome-regular-file-alt: [Code reference](../../reference/tools/#vasttools.tools.gen_mocs_epoch).
+:fontawesome-regular-file-lines: [Code reference](../../reference/tools/#vasttools.tools.gen_mocs_epoch).
This function creates all MOCs and STMOCs for the provided epoch, and a new complete Pilot STMOC. It *should not* be run in the `vasttools/data/mocs` directory. Instead, users should run it in a separate directory, check the output and then manually copy the files across.
The arguments to this function is the path to the fits file.
@@ -121,7 +121,7 @@ The arguments to this function is the path to the fits file.
### Plotting niceties
#### offset_postagestamp_axes
-:fontawesome-regular-file-alt: [Code reference](../../reference/tools/#vasttools.tools.offset_postagestamp_axes).
+:fontawesome-regular-file-lines: [Code reference](../../reference/tools/#vasttools.tools.offset_postagestamp_axes).
This function updates a figure to display the axis labels as offsets from a central coordinate, rather than in absolute Right Ascension and Declination.
The required arguments to this function are the axis and the central coordinate. Refer to the Code Reference for information on all other the arguments.
@@ -147,7 +147,7 @@ The required arguments to this function are the axis and the central coordinate.
#### wise_color_color_plot
-:fontawesome-regular-file-alt: [Code reference](../../reference/tools/#vasttools.tools.wise_color_color_plot).
+:fontawesome-regular-file-lines: [Code reference](../../reference/tools/#vasttools.tools.wise_color_color_plot).
This function returns a WISE color-color figure with common object classification regions
drawn as patches. A set of default object classes are provided, see
diff --git a/docs/theme/main.html b/docs/theme/main.html
index 2aa1157c..ee471d50 100644
--- a/docs/theme/main.html
+++ b/docs/theme/main.html
@@ -28,10 +28,10 @@
{% block announce %}
Version 3.1.1 released! Includes access to post-processed data, various bug fixes and more 🙌 Check the release notes! 👀
diff --git a/mkdocs.yml b/mkdocs.yml
index bc1a04a2..bcbb5e9f 100644
--- a/mkdocs.yml
+++ b/mkdocs.yml
@@ -12,6 +12,9 @@ dev_addr: localhost:8008
docs_dir: docs
site_dir: docs_build
+watch:
+ - vasttools
+
theme:
name: material
favicon: img/favicon.png
@@ -53,18 +56,18 @@ markdown_extensions:
- pymdownx.caret
- pymdownx.details
- pymdownx.inlinehilite
- - pymdownx.tabbed
+ - pymdownx.tabbed:
+ alternate_style: true
- pymdownx.superfences
- pymdownx.highlight
- pymdownx.tabbed
- pymdownx.emoji:
- emoji_index: !!python/name:materialx.emoji.twemoji
- emoji_generator: !!python/name:materialx.emoji.to_svg
+ emoji_index: !!python/name:material.extensions.emoji.twemoji
+ emoji_generator: !!python/name:material.extensions.emoji.to_svg
- toc:
toc_depth: 4
permalink: true
- codehilite
- - lightgallery
nav:
- Home: index.md
@@ -140,8 +143,6 @@ plugins:
show_source: true
setup_commands:
- "import os"
- watch:
- - vasttools
- mknotebooks
extra:
diff --git a/poetry.lock b/poetry.lock
index 3a223076..460c42b2 100644
--- a/poetry.lock
+++ b/poetry.lock
@@ -150,37 +150,56 @@ test = ["dateparser (==1.*)", "pre-commit", "pytest", "pytest-cov", "pytest-mock
[[package]]
name = "astropy"
-version = "4.3.1"
+version = "5.2.2"
description = "Astronomy and astrophysics core library"
optional = false
-python-versions = ">=3.7"
+python-versions = ">=3.8"
files = [
- {file = "astropy-4.3.1-cp37-cp37m-macosx_10_9_x86_64.whl", hash = "sha256:a0764d7f68034c584dda8d1c9cc4357ade05cec4c1134db43bce804fcf656ff1"},
- {file = "astropy-4.3.1-cp37-cp37m-manylinux_2_12_i686.manylinux2010_i686.whl", hash = "sha256:ce1095e385ec74c655866eacd1853535fbc2dd2c42a8188503fe9a68b8a98ea0"},
- {file = "astropy-4.3.1-cp37-cp37m-manylinux_2_12_x86_64.manylinux2010_x86_64.whl", hash = "sha256:9a01cc7b9d50f265d5d77e1f7206cda22c62720f5bed63158ee56440708848ea"},
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- {file = "astropy-4.3.1.tar.gz", hash = "sha256:2d3951223b4eb7f368fcad8c8340d27374c5d8e3b635a636275acdb38f35cd51"},
+ {file = "astropy-5.2.2-cp310-cp310-macosx_10_9_x86_64.whl", hash = "sha256:66522e897daf3766775c00ef5c63b69beb0eb359e1f45d18745d0f0ca7f29cc1"},
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toml = ["tomli"]
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+ {file = "vaex_core-4.17.1-cp39-cp39-manylinux_2_17_x86_64.manylinux2014_x86_64.whl", hash = "sha256:8565eb9d1c067ace8d40bd0fea5c092198185b550bcaf6346eef2ce78edece62"},
+ {file = "vaex_core-4.17.1-cp39-cp39-musllinux_1_1_x86_64.whl", hash = "sha256:c1209e3395b085d46467067205e13f7ed46b0ab97635ffc9e7e936ae05d6ab1a"},
+ {file = "vaex_core-4.17.1-cp39-cp39-win_amd64.whl", hash = "sha256:5629402fb440376a5966841ee19cb72f0ef9c00aaaa2243c6bb2ced6ff80b36a"},
]
[package.dependencies]
@@ -4908,7 +4929,7 @@ nest-asyncio = ">=1.3.3"
numpy = ">=1.16"
pandas = "*"
progressbar2 = "*"
-pyarrow = ">=3.0"
+pyarrow = ">=5.0.0"
pydantic = ">=1.8.0"
pyyaml = "*"
requests = "*"
@@ -4921,13 +4942,13 @@ all = ["gcsfs (>=0.6.2)", "s3fs"]
[[package]]
name = "vaex-hdf5"
-version = "0.7.0"
+version = "0.14.1"
description = "hdf5 file support for vaex"
optional = false
python-versions = "*"
files = [
- {file = "vaex-hdf5-0.7.0.tar.gz", hash = "sha256:73f898f9bc3fa5c61a67fb31a85be296bbd37d157cdf2a1d48d22f0ccad024c6"},
- {file = "vaex_hdf5-0.7.0-py3-none-any.whl", hash = "sha256:1b7c93f8da507189f73e1d1c2eec346163b88a7aaa4e62595cc58e95fc8ba640"},
+ {file = "vaex-hdf5-0.14.1.tar.gz", hash = "sha256:ac6ab69b2d6a1a3b0aec14a6314b743dcda0247cffa1fb9266b1b1839319ec81"},
+ {file = "vaex_hdf5-0.14.1-py3-none-any.whl", hash = "sha256:490c8337217e6005390dd574111d5d6d1344c2a6403e19b366c81a395d559293"},
]
[package.dependencies]
@@ -5045,6 +5066,17 @@ files = [
[package.extras]
test = ["pytest (>=6.0.0)", "setuptools (>=65)"]
+[[package]]
+name = "xyzservices"
+version = "2024.6.0"
+description = "Source of XYZ tiles providers"
+optional = false
+python-versions = ">=3.8"
+files = [
+ {file = "xyzservices-2024.6.0-py3-none-any.whl", hash = "sha256:fecb2508f0f2b71c819aecf5df2c03cef001c56a4b49302e640f3b34710d25e4"},
+ {file = "xyzservices-2024.6.0.tar.gz", hash = "sha256:58c1bdab4257d2551b9ef91cd48571f77b7c4d2bc45bf5e3c05ac97b3a4d7282"},
+]
+
[[package]]
name = "y-py"
version = "0.6.2"
@@ -5164,5 +5196,5 @@ test = ["big-O", "importlib-resources", "jaraco.functools", "jaraco.itertools",
[metadata]
lock-version = "2.0"
-python-versions = "^3.8.0"
-content-hash = "02b46107d602ebb4a7e7b8e82d8e2dd6fbb4ae1cf24907adf15bbe5bae2251d5"
+python-versions = ">=3.8.0,<3.11"
+content-hash = "83f21dcce843cdd54e6572eddd365544755fa71b04766ca288e9af1b80023fa0"
diff --git a/pyproject.toml b/pyproject.toml
index 5a54da1a..ef9c844f 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -4,58 +4,55 @@ version = "3.1.1-dev"
description = "Python module to interact with ASKAP VAST data."
license = "MIT"
homepage = "https://github.com/askap-vast/vasttools/"
-authors = ["Adam Stewart ", "Dougal Dobie "]
+authors = ["Adam Stewart ", "Dougal Dobie "]
include = ["vasttools/data", "example_notebooks"]
[tool.poetry.dependencies]
-python = "^3.8.0"
-astropy = "^4.2"
-astroquery = "^0.4.1"
-bokeh = "^2.1.1"
-colorcet = "^2.0.2"
-colorlog = "^4.1.0"
-dask = {extras = ["dataframe"], version = "^2021.10.0"}
+python = ">=3.8.0,<3.11"
+astropy = "^5.2"
+astroquery = "^0"
+bokeh = "^3.1"
+colorcet = "^3.1"
+colorlog = "^6.1"
+dask = {version = "^2022.01.0", extras = ["dataframe"]}
forced-phot = { git = "https://github.com/askap-vast/forced_phot.git" }
-matplotlib = ">=3.2.1 <3.7"
-mocpy = "^0.8.4"
+matplotlib = "^3.7.0"
+mocpy = "^0.11"
multiprocessing-logging = "^0.3.1"
numexpr = "^2.7.1"
numpy = "~1.22.1"
-pandas = "^1.1.4"
-pyarrow = "^3.0.0"
-radio-beam = "^0.3.2"
-scipy = "^1.4.1"
+pandas = "<2.0"
+pyarrow = "^17.0"
+radio-beam = "^0.3"
+scipy = "^1.4"
tables = "^3.6.1"
-tabulate = "^0.8.7"
-vaex-astro = "^0.8.0"
-vaex-core = "^4.5.0"
-vaex-hdf5 = "^0.7.0"
+tabulate = "^0"
+vaex-core = "^4.17"
+vaex-hdf5 = "^0.14"
healpy = "^1.15.0"
svgpath2mpl = "^1.0.0"
setuptools = "^70.0.0"
pydantic = "<2.0.0"
-[tool.poetry.dev-dependencies]
+[tool.poetry.group.dev.dependencies]
ipdb = "^0.13.6"
jupyterlab = "^3.6.7"
jupyterlab-execute-time = "^2.0.2"
jupyterlab-system-monitor = "^0.8.0"
-mkdocs = "1.3.1"
-mkdocs-material = "^7.3.0"
-mkdocstrings = "^0.17.0"
+mkdocs-material = "^9.4"
+mkdocstrings = {version="^0.25", extras = ["python"]}
mkdocs-minify-plugin = "^0.4.1"
mkdocs-material-extensions = "^1.0.3"
-mkdocs-gen-files = "^0.3.3"
-mknotebooks = "^0.7.1"
+mkdocs-gen-files = "^0.5"
+mknotebooks = "^0.8"
Pygments = "^2.15.0"
-lightgallery = "^0.5"
-mkdocs-git-revision-date-localized-plugin = "^0.10.0"
-pytest = "^6.2.4"
-pytest-mock = "^3.6.1"
-autopep8 = "^1.5.7"
-pytest-cov = "^2.12.1"
-flake8 = "^4.0.1"
+mkdocs-git-revision-date-localized-plugin = "^1.2"
+pytest = "^8.3"
+pytest-mock = "^3.14"
+autopep8 = "^2.3"
+pytest-cov = "^5.0"
jinja2 = "3.0.3"
+flake8 = {version="^7.1", python=">=3.8.1,<3.11"}
[tool.poetry.scripts]
build_lightcurves = "vasttools.bin.build_lightcurves:main"
diff --git a/tests/test_tools.py b/tests/test_tools.py
index ee791ea3..f00bec4a 100644
--- a/tests/test_tools.py
+++ b/tests/test_tools.py
@@ -160,7 +160,8 @@ def dummy_stmoc() -> Union[MOC, STMOC]:
def dummy_ax(dummy_fits_open):
hdu = dummy_fits_open[0]
wcs = WCS(hdu.header)
- ax = plt.subplot(projection=wcs)
+ fig = plt.figure()
+ ax = fig.add_subplot(projection=wcs)
return ax
@@ -432,8 +433,8 @@ def test_gen_mocs_image(
mocker_stmoc_write.assert_called_once_with(Path(stmoc_file),
overwrite=True)
- assert stmoc.max_time.jd == end.jd
- assert stmoc.min_time.jd == start.jd
+ assert stmoc.max_time.isclose(end, atol=1e-5 * u.s)
+ assert stmoc.min_time.isclose(start, atol=1e-5 * u.s)
def test_gen_mocs_epoch(dummy_moc: MOC,
diff --git a/vasttools/moc.py b/vasttools/moc.py
index c47caa72..607f360a 100644
--- a/vasttools/moc.py
+++ b/vasttools/moc.py
@@ -42,6 +42,7 @@ def load_pilot_stmoc(self) -> STMOC:
stmoc_name
) as stmoc_path:
stmoc_path = stmoc_path.resolve()
+ print(stmoc_path)
stmoc = STMOC.from_fits(stmoc_path)
@@ -220,7 +221,7 @@ def _load_full_survey_footprint(self, order: int = 10) -> MOC:
return survey_moc.degrade_to_order(order)
- def load_survey_footprint(self, survey, order: int = 10) -> MOC:
+ def load_survey_footprint(self, survey: str, order: int = 10) -> MOC:
"""
Load the footprint of either the pilot or full VAST surveys
diff --git a/vasttools/pipeline.py b/vasttools/pipeline.py
index b9203f89..29cb4146 100644
--- a/vasttools/pipeline.py
+++ b/vasttools/pipeline.py
@@ -4,6 +4,8 @@
HOST_NCPU (int): The number of CPU found on the host using 'cpu_count()'.
"""
+from __future__ import annotations
+
import numexpr
import os
import warnings
@@ -62,6 +64,7 @@ class PipelineDirectoryError(Exception):
"""
pass
+
class MeasPairsDoNotExistError(Exception):
"""
An error to indicate that the measurement pairs do not exist for a run.
@@ -167,12 +170,12 @@ def __init__(
self.logger = logging.getLogger('vasttools.pipeline.PipeRun')
self.logger.debug('Created PipeRun instance')
-
+
self._measurement_pairs_exists = self._check_measurement_pairs_file()
def _check_measurement_pairs_file(self):
measurement_pairs_exists = True
-
+
for filepath in self.measurement_pairs_file:
if not os.path.isfile(filepath):
self.logger.warning(f"Measurement pairs file ({filepath}) does"
@@ -182,10 +185,10 @@ def _check_measurement_pairs_file(self):
measurement_pairs_exists = False
return measurement_pairs_exists
-
+
def combine_with_run(
- self, other_PipeRun, new_name: Optional[str] = None
- ):
+ self, other_PipeRun: PipeRun, new_name: Optional[str] = None
+ ) -> PipeRun:
"""
Combines the output of another PipeRun object with the PipeRun
from which this method is being called from.
@@ -196,12 +199,12 @@ def combine_with_run(
returned.
Args:
- other_PipeRun (PipeRun): The other pipeline run to merge.
+ other_PipeRun: The other pipeline run to merge.
new_name: If not None then the PipeRun attribute 'name'
is changed to the given value.
Returns:
- PipeRun: The self object with the other pipeline run added.
+ The self object with the other pipeline run added.
"""
self.images = pd.concat(
@@ -251,7 +254,7 @@ def combine_with_run(
if orig_run_pairs_exist and other_run_pairs_exist:
for i in other_PipeRun.measurement_pairs_file:
self.measurement_pairs_file.append(i)
-
+
elif orig_run_pairs_exist:
self.logger.warning("Not combining measurement pairs because they "
" do not exist for the new run."
@@ -293,8 +296,7 @@ def get_sources_skycoord(
Must be an astropy.unit value.
Returns:
- Skycoord object of the sources. A
- `astropy.coordinates.sky_coordinate.SkyCoord` instance.
+ A SkyCoord containing the source coordinates.
"""
if user_sources is None:
the_sources = self.sources
@@ -343,7 +345,7 @@ def get_source(
pipeline measurements are used.
Returns:
- vast tools Source object.
+ A vast-tools `Source` object corresponding to the requested source.
"""
if user_measurements is None:
@@ -445,10 +447,10 @@ def get_source(
def _raise_if_no_pairs(self):
if not self._measurement_pairs_exists:
- raise MeasPairsDoNotExistError("This method cannot be used as "
- "the measurement pairs are not "
- "available for this pipeline run."
- )
+ raise MeasPairsDoNotExistError("This method cannot be used as "
+ "the measurement pairs are not "
+ "available for this pipeline run."
+ )
def load_two_epoch_metrics(self) -> None:
"""
@@ -469,7 +471,7 @@ def load_two_epoch_metrics(self) -> None:
MeasPairsDoNotExistError: The measurement pairs file(s) do not
exist for this run
"""
-
+
self._raise_if_no_pairs()
image_ids = self.images.sort_values(by='datetime').index.tolist()
@@ -630,7 +632,7 @@ def check_for_planets(self) -> pd.DataFrame:
Returns:
DataFrame with list of planet positions. It will be empty if no
- planets are found. A `pandas.core.frame.DataFrame` instance.
+ planets are found. A `pandas.core.frame.DataFrame` instance.
"""
from vasttools import ALLOWED_PLANETS
ap = ALLOWED_PLANETS.copy()
@@ -717,7 +719,7 @@ def check_for_planets(self) -> pd.DataFrame:
return result
- def filter_by_moc(self, moc: mocpy.MOC):
+ def filter_by_moc(self, moc: mocpy.MOC) -> PipeAnalysis:
"""
Filters the PipeRun object to only contain the sources that are
located within the provided moc area.
@@ -726,7 +728,7 @@ def filter_by_moc(self, moc: mocpy.MOC):
moc: MOC instance for which to filter the run by.
Returns:
- PipeAnalysis: new_PipeRun
+ A new `PipeRun` object containing the sources within the MOC.
"""
source_mask = moc.contains(
self.sources_skycoord.ra, self.sources_skycoord.dec)
@@ -797,7 +799,7 @@ def create_moc(
a large run.
Returns:
- MOC object.
+ MOC object containing the area covered by the pipeline run.
"""
images_to_use = self.images.drop_duplicates(
'skyreg_id'
@@ -1092,12 +1094,12 @@ def recalc_sources_df(
Returns:
The regenerated sources_df. A `pandas.core.frame.DataFrame`
instance.
-
+
Raises:
MeasPairsDoNotExistError: The measurement pairs file(s) do not
exist for this run
"""
-
+
self._raise_if_no_pairs()
# Two epoch metrics
@@ -1284,7 +1286,6 @@ def recalc_sources_df(
).rename(columns={'to_source_id': 'n_relations'})
sources_df = sources_df.join(sources_df_relations)
-
# nearest neighbour
sources_sky_coord = gen_skycoord_from_df(
sources_df, ra_col='wavg_ra', dec_col='wavg_dec'
@@ -1553,7 +1554,7 @@ def _plot_epoch_pair_matplotlib(
use_int_flux: bool = False,
remove_two_forced: bool = False,
plot_style: str = 'a'
- ) -> plt.figure:
+ ) -> matplotlib.figure.Figure:
"""
Plot the results of the two epoch analysis using matplotlib. Currently
this can only plot one epoch pair at a time.
@@ -1649,7 +1650,7 @@ def _plot_epoch_pair_matplotlib(
epoch_pair_id, td_days
)
number_string = "Candidates: {}/{} ({:.2f} %)".format(
- num_candidates, num_pairs, (100.*num_candidates/num_pairs)
+ num_candidates, num_pairs, (100. * num_candidates / num_pairs)
)
ax.text(
0.6, 0.05, date_string + '\n' + number_string,
@@ -1670,7 +1671,7 @@ def plot_two_epoch_pairs(
remove_two_forced: bool = False,
plot_type: str = 'bokeh',
plot_style: str = 'a'
- ) -> Union[Model, plt.figure]:
+ ) -> Union[Model, matplotlib.figure.Figure]:
"""
Adapted from code written by Andrew O'Brien.
Plot the results of the two epoch analysis. Currently this can only
@@ -1803,7 +1804,7 @@ def run_two_epoch_analysis(
MeasPairsDoNotExistError: The measurement pairs file(s) do not
exist for this run
"""
-
+
self._raise_if_no_pairs()
if not self._loaded_two_epoch_metrics:
@@ -1945,7 +1946,7 @@ def eta_v_diagnostic_plot(
self, eta_cutoff: float, v_cutoff: float,
df: Optional[pd.DataFrame] = None,
use_int_flux: bool = False
- ) -> plt.figure:
+ ) -> matplotlib.figure.Figure:
"""
Adapted from code written by Antonia Rowlinson.
Produces the eta, V 'diagnostic plot'
@@ -2061,7 +2062,7 @@ def _plot_eta_v_matplotlib(
eta_cutoff: float,
v_cutoff: float,
use_int_flux: bool = False
- ) -> plt.figure:
+ ) -> matplotlib.figure.Figure:
"""
Adapted from code written by Antonia Rowlinson.
Produces the eta, V candidates plot
@@ -2100,7 +2101,7 @@ def _plot_eta_v_matplotlib(
fontP.set_size('large')
left, width = 0.1, 0.65
bottom, height = 0.1, 0.65
- bottom_h = left_h = left+width+0.02
+ bottom_h = left_h = left + width + 0.02
rect_scatter = [left, bottom, width, height]
rect_histx = [left, bottom_h, width, 0.2]
rect_histy = [left_h, bottom, 0.2, height]
@@ -2140,7 +2141,7 @@ def _plot_eta_v_matplotlib(
ymin = int(min(y) - 1.1)
ymax = int(max(y) + 1.1)
xvals = range(xmin, xmax)
- xtxts = [r'$10^{'+str(a)+'}$' for a in xvals]
+ xtxts = [r'$10^{' + str(a) + '}$' for a in xvals]
yvals = range(ymin, ymax)
ytxts = [r'$10^{' + str(a) + '}$' for a in yvals]
axScatter.set_xlim([xmin, xmax])
@@ -2245,8 +2246,8 @@ def _plot_eta_v_bokeh(
PLOT_WIDTH = 700
PLOT_HEIGHT = PLOT_WIDTH
fig = figure(
- plot_width=PLOT_WIDTH,
- plot_height=PLOT_HEIGHT,
+ width=PLOT_WIDTH,
+ height=PLOT_HEIGHT,
aspect_scale=1,
x_axis_type="log",
y_axis_type="log",
@@ -2269,8 +2270,8 @@ def _plot_eta_v_bokeh(
# axis histograms
# filter out any forced-phot points for these
x_hist = figure(
- plot_width=PLOT_WIDTH,
- plot_height=100,
+ width=PLOT_WIDTH,
+ height=100,
x_range=fig.x_range,
y_axis_type=None,
x_axis_type="log",
@@ -2298,8 +2299,8 @@ def _plot_eta_v_bokeh(
fig.add_layout(x_hist_sigma_span)
y_hist = figure(
- plot_height=PLOT_HEIGHT,
- plot_width=100,
+ height=PLOT_HEIGHT,
+ width=100,
y_range=fig.y_range,
x_axis_type=None,
y_axis_type="log",
@@ -2346,8 +2347,16 @@ def run_eta_v_analysis(
use_int_flux: bool = False, plot_type: str = 'bokeh',
diagnostic: bool = False
) -> Union[
- Tuple[float, float, pd.DataFrame, plt.figure, plt.figure],
- Tuple[float, float, pd.DataFrame, gridplot, plt.figure]
+ Tuple[float,
+ float,
+ pd.DataFrame,
+ matplotlib.figure.Figure,
+ matplotlib.figure.Figure],
+ Tuple[float,
+ float,
+ pd.DataFrame,
+ gridplot,
+ matplotlib.figure.Figure]
]:
"""
Run the eta, v analysis on the pipeline run, with optional
@@ -2375,8 +2384,8 @@ def run_eta_v_analysis(
Returns:
Tuple containing the eta cutoff value, the v cutoff value,
- dataframe of candidates, candidates plot and, if selected, the
- diagnostic plot.
+ dataframe of candidates, candidates plot and, if selected, the
+ diagnostic plot.
Raise:
Exception: Entered `plot_type` is not a valid plot type.
diff --git a/vasttools/source.py b/vasttools/source.py
index 80bfcbc0..1ff3af23 100644
--- a/vasttools/source.py
+++ b/vasttools/source.py
@@ -35,7 +35,7 @@
from astropy.time import Time
from astropy.table import Table
from astroquery.simbad import Simbad
-from astroquery.ned import Ned
+from astroquery.ipac.ned import Ned
from astroquery.casda import Casda
from astropy.stats import sigma_clipped_stats
from astroquery.skyview import SkyView
@@ -331,7 +331,7 @@ def plot_lightcurve(
use_forced_for_all: bool = False,
hide_legend: bool = False,
plot_dpi: int = 150
- ) -> Union[None, plt.Figure]:
+ ) -> Union[None, matplotlib.figure.Figure]:
"""
Plot source lightcurves and save to file
@@ -362,7 +362,7 @@ def plot_lightcurve(
Returns:
None if save is `True` or the matplotlib figure if save is
- `False`.
+ `False`.
Raises:
SourcePlottingError: Source does not have any forced fits when the
@@ -449,7 +449,7 @@ def plot_lightcurve(
freqs = list(grouped_df.groups.keys())
# Colours for each frequency
- freq_cmap = plt.cm.get_cmap('viridis')
+ freq_cmap = matplotlib.colormaps.get_cmap('viridis')
cNorm = matplotlib.colors.Normalize(
vmin=min(freqs), vmax=max(freqs) * 1.1)
scalarMap = matplotlib.cm.ScalarMappable(norm=cNorm, cmap=freq_cmap)
@@ -901,7 +901,7 @@ def show_png_cutout(
offset_axes: Use offset, rather than absolute, axis labels.
Returns:
- Figure object.
+ The cutout Figure.
"""
fig = self.make_png(
@@ -1360,7 +1360,7 @@ def show_all_png_cutouts(
hide_epoch_labels: bool = False,
plot_dpi: int = 150,
offset_axes: bool = True
- ) -> Union[None, plt.figure]:
+ ) -> Union[None, matplotlib.figure.Figure]:
"""
Creates a grid plot showing the source in each epoch.
@@ -1602,7 +1602,7 @@ def _gen_overlay_collection(
patches = [Ellipse(
coordinates[i], hh[i], ww[i],
- aa[i]) for i in range(len(coordinates))]
+ angle=aa[i]) for i in range(len(coordinates))]
collection = PatchCollection(
patches,
facecolors="None",
@@ -1626,7 +1626,7 @@ def skyview_contour_plot(
size: Optional[Angle] = None,
force: bool = False,
plot_dpi: int = 150,
- ) -> Union[None, plt.figure]:
+ ) -> Union[None, matplotlib.figure.Figure]:
"""
Fetches a FITS file from SkyView of the requested survey at
the source location and overlays ASKAP contours.
@@ -1788,7 +1788,7 @@ def make_png(
norms: Optional[ImageNormalize] = None,
plot_dpi: int = 150,
offset_axes: bool = True
- ) -> Union[None, plt.figure]:
+ ) -> Union[None, matplotlib.figure.Figure]:
"""
Save a PNG of the image postagestamp.
diff --git a/vasttools/survey.py b/vasttools/survey.py
index ddef784d..59408b08 100644
--- a/vasttools/survey.py
+++ b/vasttools/survey.py
@@ -361,10 +361,7 @@ def __init__(
def get_paths_and_names(self) -> None:
"""
- Configure the file names if they have no been provided.
-
- Args:
- None
+ Configure the file names if they have not been provided.
Returns:
None
diff --git a/vasttools/tools.py b/vasttools/tools.py
index 16aa1c8e..c2b7976d 100644
--- a/vasttools/tools.py
+++ b/vasttools/tools.py
@@ -45,7 +45,7 @@ def skymap2moc(filename: str, cutoff: float) -> MOC:
Raises:
ValueError: Credible level cutoff must be between 0 and 1.
- Exception: Path does not exist.
+ Exception: Skymap path does not exist.
"""
skymap = Path(filename)
@@ -362,7 +362,7 @@ def create_fields_metadata(epoch_num: str,
None
Raises:
- Exception: Path does not exist.
+ Exception: Database path does not exist.
"""
if isinstance(outdir, str):
@@ -464,7 +464,8 @@ def gen_mocs_image(fits_file: str,
The MOC and STMOC.
Raises:
- Exception: Path does not exist.
+ Exception: Output directory does not exist.
+ Exception: Fits file does not exist.
"""
if isinstance(outdir, str):
@@ -525,7 +526,7 @@ def gen_mocs_epoch(epoch: str,
None
Raises:
- Exception: Path does not exist.
+ Exception: Output directory does not exist.
"""
if isinstance(outdir, str):
@@ -691,7 +692,7 @@ class WisePatchConfig:
supported by `matplotlib.patches.PathPatch`.
annotation_text (str): Text to annotate the patch.
annotation_position (Tuple[float, float]): Position in data coordinates
- for the annotation text.
+ for the annotation text.
"""
style: Dict[str, Any]
@@ -755,7 +756,8 @@ def wise_color_color_plot(
patch_style_overrides: Optional[Dict[WiseClass, WisePatchConfig]] = None,
annotation_text_size: Union[float, str] = "x-small",
) -> matplotlib.figure.Figure:
- """Make an empty WISE color-color plot with common object classes drawn as
+ """
+ Make an empty WISE color-color plot with common object classes drawn as
patches. The patches have default styles that may be overridden. To
override a patch style, pass in a dict containing the desired style and
annotation settings. The overrides must be complete, i.e. a complete
@@ -775,17 +777,15 @@ def wise_color_color_plot(
```
Args:
- patch_style_overrides (Optional[Dict[WiseClass, WisePatchConfig]],
- optional): Override the default patch styles for the given WISE
- object class. If None, use defaults for each patch. Defaults to
- None.
- annotation_text_size (Union[float, str]): Font size for the patch
- annotations. Accepts a font size (float) or a matplotlib font scale
- string (e.g. "xx-small", "medium", "xx-large"). Defaults to
- "x-small".
+ patch_style_overrides: Override the default patch styles for the given
+ WISE object class. If None, use defaults for each patch. Defaults
+ to None.
+ annotation_text_size: Font size for the patch annotations. Accepts a
+ font size (float) or a matplotlib font scale string
+ (e.g. "xx-small", "medium", "xx-large"). Defaults to "x-small".
+
Returns:
- `matplotlib.figure.Figure`: the WISE color-color figure. Access the
- axes with the `.axes` attribute.
+ The WISE color-color figure. The axes can be accessed via `.axes`.
"""
# set the WISE object classification patch styles
if patch_style_overrides is not None:
diff --git a/vasttools/utils.py b/vasttools/utils.py
index e1161ddc..df04dae5 100644
--- a/vasttools/utils.py
+++ b/vasttools/utils.py
@@ -167,6 +167,8 @@ def crosshair() -> None:
A wrapper function to set the crosshair marker in
matplotlib using the function written by L. A. Boogaard.
+ See https://stackoverflow.com/a/16655800/5064815.
+
Returns:
None
"""
@@ -185,7 +187,7 @@ def check_file(path: str) -> bool:
Returns:
Boolean representing the file existence, 'True' if present, otherwise
- 'False'.
+ 'False'.
"""
logger = logging.getLogger()
exists = os.path.isfile(path)
@@ -322,9 +324,11 @@ def read_selavy(
) -> pd.DataFrame:
"""
Load a selavy catalogue from file. Can handle VOTables and csv files.
+
Args:
selavy_path: Path to the file.
cols: Columns to use. Defaults to None, which returns all columns.
+
Returns:
Dataframe containing the catalogue.
"""
@@ -444,9 +448,9 @@ def match_planet_to_field(
planet is considered to be in the field. Unit is degrees.
Returns:
- The group with planet location information added and
- filtered for only those which are within 'sep_thresh' degrees. Hence
- an empty dataframe could be returned.
+ The group with planet location information added and filtered for only
+ those which are within 'sep_thresh' degrees. Hence an empty
+ dataframe could be returned.
"""
if group.empty:
@@ -531,7 +535,7 @@ def gen_skycoord_from_df(
an astropy.unit value.
Returns:
- SkyCoord object
+ A SkyCoord object containing the coordinates of the requested sources.
"""
sc = SkyCoord(
df[ra_col].values, df[dec_col].values, unit=(ra_unit, dec_unit)
@@ -553,7 +557,7 @@ def pipeline_get_eta_metric(df: pd.DataFrame, peak: bool = False) -> float:
peak: Whether to use peak flux instead of integrated, defaults to
False.
- Returns eta:
+ Returns:
The eta variability metric.
"""
if df.shape[0] == 1:
@@ -582,7 +586,7 @@ def pipeline_get_variable_metrics(df: pd.DataFrame) -> pd.Series:
Returns:
The variability metrics, v_int, v_peak, eta_int and eta_peak
- as a pandas series.
+ as a pandas series.
"""
d = {}
@@ -609,13 +613,13 @@ def calculate_vs_metric(
for details, DOI: 10.3847/0004-637X/818/2/105.
Args:
- flux_a (float): flux value "A".
- flux_b (float): flux value "B".
- flux_err_a (float): error of `flux_a`.
- flux_err_b (float): error of `flux_b`.
+ flux_a: flux value "A".
+ flux_b: flux value "B".
+ flux_err_a: error of `flux_a`.
+ flux_err_b: error of `flux_b`.
Returns:
- float: the Vs metric for flux values "A" and "B".
+ The Vs metric for flux values "A" and "B".
"""
return (flux_a - flux_b) / np.hypot(flux_err_a, flux_err_b)
@@ -629,11 +633,11 @@ def calculate_m_metric(flux_a: float, flux_b: float) -> float:
DOI: 10.3847/0004-637X/818/2/105.
Args:
- flux_a (float): flux value "A".
- flux_b (float): flux value "B".
+ flux_a: flux value "A".
+ flux_b: flux value "B".
Returns:
- float: the m metric for flux values "A" and "B".
+ The m metric for flux values "A" and "B".
"""
return 2 * ((flux_a - flux_b) / (flux_a + flux_b))
@@ -669,7 +673,7 @@ def create_moc_from_fits(fits_file: str, max_depth: int = 9) -> MOC:
The MOC generated from the FITS file.
Raises:
- Exception: When the FITS file cannot be found.
+ Exception: The FITS file does not exist.
"""
if not os.path.isfile(fits_file):
raise Exception("{} does not exist".format(fits_file))
@@ -714,17 +718,21 @@ def strip_fieldnames(fieldnames: pd.Series) -> pd.Series:
return fieldnames.str.rstrip('A')
-def open_fits(fits_path: Union[str, Path], memmap: Optional[bool]=True):
+
+def open_fits(
+ fits_path: Union[str, Path],
+ memmap: Optional[bool] = True
+) -> fits.HDUList:
"""
This function opens both compressed and uncompressed fits files.
-
+
Args:
fits_path: Path to the fits file
memmap: Open the fits file with mmap.
-
+
Returns:
HDUList loaded from the fits file
-
+
Raises:
ValueError: File extension must be .fits or .fits.fz
"""