Update gcpy_env environment to install with MambaForge and to use latest package versions; Update scripts accordingly #251
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docs/environment_files/environment.yml - Move all pip dependencies to the conda/mamba section, as there are now some issues in resolving dependencies with pip. Signed-off-by: Bob Yantosca <[email protected]>
docs/environment_files/environment.yml - Remove most pegged version numbers, which cause mamba/conda installations to fail with conflicts. Signed-off-by: Bob Yantosca <[email protected]>
docs/environment_files/environment.yml - Need to peg esmf==8.1.1, esmpy==8.1.1, xesmf==0.5.1 to prevent an ImportError gcpy/plot.py - Now import PdfFileMerger from the pypdf package gcpy/util.py - Now import PdfFileWriter, PdfFileReader from the pypdf package Signed-off-by: Bob Yantosca <[email protected]>
gcpy/plot.py - PdfFileMerger is now PdfMerger - Now use None as default values. This avoids dangerous empty lists ([]) as default values for keyword arguments (so says Pylint). - Now use util.verify_variable_type to error-check arguments - Now update indendation - Trim trailing whitespace - Updated Pydoc comments gcpy/util.py - PdfFileWriter is now PdfWriter - PdfFileReader is now PdfReader - Remove "overwriteWarnings=False" from PdfReader, it's not used - PdfWriter.addPage is now PdfWriter.add_page - PdfWriter.addBookmark is now PdfWriter.add_outline_item - PdfWriter.setPageMode is now PdfWriter.page_mode Signed-off-by: Bob Yantosca <[email protected]>
gcpy/plot.py
- In routine single_panel,
- Set norm=[] if it is passed in as None
(typo: we had set sigdiff_list=[])
- In the "if xtick_positions is None:" block, now set
xtick_positions=[] by default. This fixes a "NoneType object
is not iterable" error when plotting maps.
- Now use "except ____ as exc:", which is now the recommended format
Signed-off-by: Bob Yantosca <[email protected]>
docs/environment_files/environment.yml - Added gridspec to the GCPy Python environment file, which allows us to perform regridding with gridspec/sparselt docs/environment_files/gchp_regridding.yml - Removed Signed-off-by: Bob Yantosca <[email protected]>
gcpy/plot.py
- In routine "compare_single_level",
- Set extent=None in the argument list. Then at the top of the
if extent is None, set it to [-1000, -1000, -1000, -1000].
(Suggested by Pylint)
- diff_of_diffs is now computed with a boolean test instead of
an if-else statement (suggested by Pylint)
- Comment out ref_extent and dev_extent, as Pylint detected that
these variables were unused.
- Fix "line-too-long" errors where ds_ref_reg and ds_dev_reg are
computed (suggested by Pylint).
- Comment out vmin_ref_cmp and vmin_dev_cmp, as these were detected
as unused by Pylint
- Pass absdiff.values to all_zero_or_nan (error detected by Pylint)
- Replace mpl.cm.RdBu_r with mpl.colormaps["RdBu_r"], this is the new
syntax in the most recent matplotlib version
- In routine compare_zonal_mean:
- Set pres_range=None in the argument list, and add a test to set
pres_range=[0, 2000] if pres_range is None (suggested by Pylint)
- diff_of_diffs is now computed with a boolean test instead of
an if-else statement (suggested by Pylint)
- Replace mpl.cm.RdBu_r with mpl.colormaps["RdBu_r"], this is the new
syntax in the most recent matplotlib version
- Use isinstance instead of direct type comparison
- In routine single_panel:
- Set pres_range=None in the argument list, and add a test to set
pres_range=[0, 2000] if pres_range is None (suggested by Pylint)
- Remove the "if norm is None:" block at the top of the routine,
since a similar test is done further down. This had reset the
norm object from None to [], which caused an if block further
down to not execute properly. This caused colorbar tickmarks
to render incorrectly.
- Replace "except BaseException as exc" as "except BaseException"
(suggested by Pylint)
- Also restore extent=(None, None, None, None) to the if block
that tests if extent was passed. But put this after the
"Extent is None" clause since that is now the default.
- Comment out Pydoc string
- Replace strings with f-strings where expedient
- Remove else after return (suggested by Pylint)
Signed-off-by: Bob Yantosca <[email protected]>
gcpy/constants.py
- Add ENCODING = "UTF-8", for use in open statements
gcpy/util.py
- Added code change suggested by Pylint:
- Variable names now conform to snake_case (i.e. more than 3 chars,
and separated by "_"), in particular:
- "v" -> "var"
- "ds" -> "dset"
- "dr" -> "darr"
- "f" -> "ifile" or "ofile"
- open statements are now placed in with blocks
- open statements now use encoding=ENCODING (aka UTF-8)
- In routine convert_lon, changed "format" to "fmt" to avoid
clashing with a Python reserved word
- Remove () in if blocks, they aren't necessary
- Trimmed trailing whitespace
- Remove else blocks with return statements (we de-indent instead)
- Also use verify_variable_type to check argument types
CHANGELOG.md
- Updated accordingly
Signed-off-by: Bob Yantosca <[email protected]>
gcpy/plot.py - In routine compare_single_level, use argument absdiff instead of absdiff.values when calling all_zero_or_nan. This is because absdiff is already a numpy.ndarray and not an xarray.DataArray object. Signed-off-by: Bob Yantosca <[email protected]>
gcpy/plot.py - Move code that computes vmin, vmax out of "six_plot" and into new routine compute_vmin_vmax_for_plot. Replaced else statements by "never-nesting". - Move code that computes the "norm" object out of "six_plot" and into new routine "compute_norm_for_plot". - Move code that applies colorbar tick placement and formatting out of "six_plot" and into new routine "colorbar_ticks_and_format". Also tweaked settings so that for data ranges of between 0.1 and 100, we manually set colorbar ticks. - Move the declaration of the "subplots" list from "compare_single_level" and "compare_zonal_mean" to a new routine "six_panel_subplot_names". - Add if statements to disable parallelization if n_job=1. - Added code formatting updates suggested by Pylint, where expedient - Updated comments & PyDoc headers - Trimmed trailing whitespace CHANGELOG.md - Updated accordingly Signed-off-by: Bob Yantosca <[email protected]>
gcpy/plot.py - In routine "colorbar_ticks_and_format", now use the tick label locations [vmin, (vmin+1)/2, 1, (vmax+1)/2, vmax] for ratio (dynamic range) subplots (if the data is in the range 0.1..100). This fixes an error with the colorbar tick labels from the previous commit. Signed-off-by: Bob Yantosca <[email protected]>
gcpy/plot.py - In routine "colorbar_ticks_and_format", add an if block to add the "Ref and Dev are equal throughout domain" to the absdiff plots. This was omitted during the "never-nesting" refactoring. - Remove unnecessary parentheses in if block - Update comments Signed-off-by: Bob Yantosca <[email protected]>
gcpy/plot.py
- In routine six_plot:
- Remove calls to cbar.minorticks_off() and cbar_update_ticks()
- In routine colorbar_ticks_and_format:
- Update comments
- Change "return" commands to "return cbar" in order to make sure
that the modified colorbar settings get passed back.
- Now apply cbar.set_ticks with position list and labels list.
- Also apply cbar.minorticks_off() after each call to cbar.set_ticks().
- Comment out max_abs variable, Pylint says it is unused
Signed-off-by: Bob Yantosca <[email protected]>
yantosca
added
category: Feature Request
laestrada
approved these changes
Aug 17, 2023
gcpy/plot.py - In routine colorbar_ticks_and_format, add a new internal function "ref_equals_dev" that returns True if Dev/Ref = 1. Also returns true if there are missing (NaN) values, as long as all other values are 1. This is necessary to make sure the "Ref and Dev equal throughout domain" label gets printed in ratio plots. Signed-off-by: Bob Yantosca <[email protected]>
|
Thanks @laestrada! Will do. |
yantosca
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Aug 17, 2023
This merge brings updates from PR #251 (Update gcpy_env environment to install with MambaForge and to use latest package versions; Update scripts accordingly, by @yantosca) into the feature/move-folders branch. This will facilitate merging into dev at a later time. Signed-off-by: Bob Yantosca <[email protected]>
yantosca
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Aug 17, 2023
This merge brings updates from PR #251 (Update gcpy_env environment to install with MambaForge and to use latest package versions; Update scripts accordingly, by @yantosca) into the feature/disable-parallelization branch. This will facilitate merging into dev at a later time. Signed-off-by: Bob Yantosca <[email protected]> --
hannahnesser
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Jan 22, 2024
…mbaForge) This merge brings PR geoschem#251 (Update gcpy_env environment to install with MambaForge and to use latest package versions; Update scripts accordingly, by @yantosca) into the GCPy 1.4.0 development stream. This updates the docs/environments/environment.yml file to use more modern package versions, thus eliminating the dependence on Conda 4.12, and allowing installation with MambaForge. Several updates were also made to gcpy/util.py and gcpy/plot.py due to changes in Python packages. Furthermore, we have now abstracted some code out of the six_plot routine in gcpy/plot.py into separate functions. This should make the code easier to maintain and understand. See geoschem#251 for more information. Signed-off-by: Bob Yantosca <[email protected]>
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In this PR we have done the following:
Updated the
docs/source/environment.ymlfile as follows:conda-forgeandnodefaultschannelspipxesmf==0.5.1, withesmf==8.1.1andesmpy==8.1.1, because newer versions break backward compatibility.sphinx==3.5.4and related dependencies, in order to ensure that ReadTheDocs documentation builds properlygridspec(which is needed for regridding withgridspecandsparselt)Removed the separate
docs/source/gchp_regridding.ymlenvironment file.Updated routines in
plot.pyandutil.pyfor compatibility with newer package versions:PyPDF2is nowpypdf; several function calls had to be modified.matplotlibwas updated from 3.4.2 to 3.7.2; several modifications were necessary:matplotib.colors.RdBu_r-->matplotlib.colormaps["RdBu_r"]matplotlib.colorbar.set_ticklabels->matplotlib.colorbar.set_tickswith thelabelsargument.pylint.Abstracted and "never-nested" code from routine
six_plot(inplot.py) into separate functions, for clarity.A separate documentation update will be pushed to the docs/dev branch.