Genetic and Computational Identification of a Conserved Bacterial Metabolic Module

We have experimentally and computationally defined a set of genes that form a conserved metabolic module in the α-proteobacterium Caulobacter crescentus and used this module to illustrate a schema for the propagation of pathway-level annotation across bacterial genera. Applying comprehensive forward and reverse genetic methods and genome-wide transcriptional analysis, we (1) confirmed the presence of genes involved in catabolism of the abundant environmental sugar myo-inositol, (2) defined an operon encoding an ABC-family myo-inositol transmembrane transporter, and (3) identified a novel myo-inositol regulator protein and cis-acting regulatory motif that control expression of genes in this metabolic module. Despite being encoded from non-contiguous loci on the C. crescentus chromosome, these myo-inositol catabolic enzymes and transporter proteins form a tightly linked functional group in a computationally inferred network of protein associations. Primary sequence comparison was not sufficient to confidently extend annotation of all components of this novel metabolic module to related bacterial genera. Consequently, we implemented the Graemlin multiple-network alignment algorithm to generate cross-species predictions of genes involved in myo-inositol transport and catabolism in other α-proteobacteria. Although the chromosomal organization of genes in this functional module varied between species, the upstream regions of genes in this aligned network were enriched for the same palindromic cis-regulatory motif identified experimentally in C. crescentus. Transposon disruption of the operon encoding the computationally predicted ABC myo-inositol transporter of Sinorhizobium meliloti abolished growth on myo-inositol as the sole carbon source, confirming our cross-genera functional prediction. Thus, we have defined regulatory, transport, and catabolic genes and a cis-acting regulatory sequence that form a conserved module required for myo-inositol metabolism in select α-proteobacteria. Moreover, this study describes a forward validation of gene-network alignment, and illustrates a strategy for reliably transferring pathway-level annotation across bacterial species.</p

Genetic and Computational Identification of a Conserved Bacterial Metabolic Module

We have experimentally and computationally defined a set of genes that form a conserved metabolic module in the α-proteobacterium Caulobacter crescentus and used this module to illustrate a schema for the propagation of pathway-level annotation across bacterial genera. Applying comprehensive forward and reverse genetic methods and genome-wide transcriptional analysis, we (1) confirmed the presence of genes involved in catabolism of the abundant environmental sugar myo-inositol, (2) defined an operon encoding an ABC-family myo-inositol transmembrane transporter, and (3) identified a novel myo-inositol regulator protein and cis-acting regulatory motif that control expression of genes in this metabolic module. Despite being encoded from non-contiguous loci on the C. crescentus chromosome, these myo-inositol catabolic enzymes and transporter proteins form a tightly linked functional group in a computationally inferred network of protein associations. Primary sequence comparison was not sufficient to confidently extend annotation of all components of this novel metabolic module to related bacterial genera. Consequently, we implemented the Graemlin multiple-network alignment algorithm to generate cross-species predictions of genes involved in myo-inositol transport and catabolism in other α-proteobacteria. Although the chromosomal organization of genes in this functional module varied between species, the upstream regions of genes in this aligned network were enriched for the same palindromic cis-regulatory motif identified experimentally in C. crescentus. Transposon disruption of the operon encoding the computationally predicted ABC myo-inositol transporter of Sinorhizobium meliloti abolished growth on myo-inositol as the sole carbon source, confirming our cross-genera functional prediction. Thus, we have defined regulatory, transport, and catabolic genes and a cis-acting regulatory sequence that form a conserved module required for myo-inositol metabolism in select α-proteobacteria. Moreover, this study describes a forward validation of gene-network alignment, and illustrates a strategy for reliably transferring pathway-level annotation across bacterial species

xCDAT/xcdat: v0.4.0

&lt;p&gt;v0.4.0 (9 November 2022)&lt;/p&gt; &lt;p&gt;This minor release includes a feature update to support datasets that have &lt;em&gt;N&lt;/em&gt; dimensions mapped to &lt;em&gt;N&lt;/em&gt; coordinates to represent an axis. This means &lt;code&gt;xcdat&lt;/code&gt; APIs are able to intelligently select which axis&#39;s coordinates and bounds to work with if multiple are present within the dataset. Decoding time is now a lazy operation, leading to significant upfront runtime improvements when opening datasets with &lt;code&gt;decode_times=True&lt;/code&gt;.&lt;/p&gt; &lt;p&gt;A new notebook called &quot;A Gentle Introduction to xCDAT&quot; was added to the documentation gallery to help guide new xarray/xcdat users. xCDAT is now hosted on Zenodo with a DOI for citations.&lt;/p&gt; &lt;p&gt;There are various bug fixes for bounds, naming of spatial weights, and a missing flag for &lt;code&gt;xesmf&lt;/code&gt; that broke curvilinear regridding.&lt;/p&gt; &lt;p&gt;Features&lt;/p&gt; &lt;ul&gt; &lt;li&gt;Support for N axis dimensions mapped to N coordinates by @tomvothecoder and @pochedls in &lt;a href="https://github.com/xCDAT/xcdat/pull/343"&gt;https://github.com/xCDAT/xcdat/pull/343&lt;/a&gt; &lt;ul&gt; &lt;li&gt;Rename &lt;code&gt;get_axis_coord()&lt;/code&gt; to &lt;code&gt;get_dim_coords()&lt;/code&gt; and &lt;code&gt;get_axis_dim()&lt;/code&gt; to &lt;code&gt;get_dim_keys()&lt;/code&gt;&lt;/li&gt; &lt;li&gt;Update spatial and temporal accessor class methods to refer to the dimension coordinate variable on the data_var being operated on, rather than the parent dataset&lt;/li&gt; &lt;/ul&gt; &lt;/li&gt; &lt;li&gt;Decoding times (&lt;code&gt;decode_time()&lt;/code&gt;) is now a lazy operation, which results in significant runtime improvements by @tomvothecoder in &lt;a href="https://github.com/xCDAT/xcdat/pull/343"&gt;https://github.com/xCDAT/xcdat/pull/343&lt;/a&gt;&lt;/li&gt; &lt;/ul&gt; &lt;p&gt;Bug Fixes&lt;/p&gt; &lt;ul&gt; &lt;li&gt;Fix &lt;code&gt;add_bounds()&lt;/code&gt; not ignoring 0-dim singleton coords by @tomvothecoder and @pochedls in &lt;a href="https://github.com/xCDAT/xcdat/pull/343"&gt;https://github.com/xCDAT/xcdat/pull/343&lt;/a&gt;&lt;/li&gt; &lt;li&gt;Fix name of spatial weights with singleton coord by @tomvothecoder in &lt;a href="https://github.com/xCDAT/xcdat/pull/379"&gt;https://github.com/xCDAT/xcdat/pull/379&lt;/a&gt;&lt;/li&gt; &lt;li&gt;Fixes &lt;code&gt;xesmf&lt;/code&gt; flag that was missing which broke curvilinear regridding by @jasonb5 and @pochedls in &lt;a href="https://github.com/xCDAT/xcdat/pull/374"&gt;https://github.com/xCDAT/xcdat/pull/374&lt;/a&gt;&lt;/li&gt; &lt;/ul&gt; &lt;p&gt;Documentation&lt;/p&gt; &lt;ul&gt; &lt;li&gt;Add FAQs section for temporal metadata by @tomvothecoder in &lt;a href="https://github.com/xCDAT/xcdat/pull/383"&gt;https://github.com/xCDAT/xcdat/pull/383&lt;/a&gt;&lt;/li&gt; &lt;li&gt;Add gentle introduction notebook by @tomvothecoder in &lt;a href="https://github.com/xCDAT/xcdat/pull/373"&gt;https://github.com/xCDAT/xcdat/pull/373&lt;/a&gt;&lt;/li&gt; &lt;li&gt;Link repo to Zenodo and upload GitHub releases by @tomvothecoder in &lt;a href="https://github.com/xCDAT/xcdat/pull/367"&gt;https://github.com/xCDAT/xcdat/pull/367&lt;/a&gt;&lt;/li&gt; &lt;li&gt;Update project overview, FAQs, and add a link to xarray tutorials by @tomvothecoder in &lt;a href="https://github.com/xCDAT/xcdat/pull/365"&gt;https://github.com/xCDAT/xcdat/pull/365&lt;/a&gt;&lt;/li&gt; &lt;li&gt;Update feature list, add metadata interpretation to FAQs, and add &lt;code&gt;ipython&lt;/code&gt; syntax highlighting for notebooks by @tomvothecoder in &lt;a href="https://github.com/xCDAT/xcdat/pull/362"&gt;https://github.com/xCDAT/xcdat/pull/362&lt;/a&gt;&lt;/li&gt; &lt;/ul&gt; &lt;p&gt;DevOps&lt;/p&gt; &lt;ul&gt; &lt;li&gt;Update release-drafter template by @tomvothecoder in &lt;a href="https://github.com/xCDAT/xcdat/pull/371"&gt;https://github.com/xCDAT/xcdat/pull/371&lt;/a&gt; and &lt;a href="https://github.com/xCDAT/xcdat/pull/370"&gt;https://github.com/xCDAT/xcdat/pull/370&lt;/a&gt;&lt;/li&gt; &lt;li&gt;Automate release notes generation by @tomvothecoder in &lt;a href="https://github.com/xCDAT/xcdat/pull/368"&gt;https://github.com/xCDAT/xcdat/pull/368&lt;/a&gt;&lt;/li&gt; &lt;/ul&gt; &lt;p&gt;&lt;strong&gt;Full Changelog&lt;/strong&gt;: &lt;a href="https://github.com/xCDAT/xcdat/compare/v0.3.3...v0.4.0"&gt;https://github.com/xCDAT/xcdat/compare/v0.3.3...v0.4.0&lt;/a&gt;&lt;/p&gt

xCDAT/xcdat: v0.5.0

&lt;p&gt;v0.5.0 (27 March 2023)&lt;/p&gt; &lt;p&gt;This long-awaited minor release includes feature updates to support an optional user-specified climatology reference period when calculating climatologies and departures, support for opening datasets using the &lt;code&gt;directory&lt;/code&gt; key of the legacy CDAT &lt;a href="https://cdms.readthedocs.io/en/latest/manual/cdms_6.html"&gt;Climate Data Markup Language (CDML)&lt;/a&gt; format (an XML dialect), and improved support for using custom time coordinates in temporal APIs.&lt;/p&gt; &lt;p&gt;This release also includes a bug fix for singleton coordinates breaking the &lt;code&gt;swap_lon_axis()&lt;/code&gt; function. Additionally, Jupyter Notebooks for presentations and demos have been added to the documentation.&lt;/p&gt; &lt;p&gt;Features&lt;/p&gt; &lt;ul&gt; &lt;li&gt;Update departures and climatology APIs with reference period by @tomvothecoder in &lt;a href="https://github.com/xCDAT/xcdat/pull/417"&gt;https://github.com/xCDAT/xcdat/pull/417&lt;/a&gt;&lt;/li&gt; &lt;li&gt;Wrap open_dataset and open_mfdataset to flexibly open datasets by @pochedls in &lt;a href="https://github.com/xCDAT/xcdat/pull/385"&gt;https://github.com/xCDAT/xcdat/pull/385&lt;/a&gt;&lt;/li&gt; &lt;li&gt;Add better support for using custom time coordinates in temporal APIs by @tomvothecoder in &lt;a href="https://github.com/xCDAT/xcdat/pull/415"&gt;https://github.com/xCDAT/xcdat/pull/415&lt;/a&gt;&lt;/li&gt; &lt;/ul&gt; &lt;p&gt;Bug Fixes&lt;/p&gt; &lt;ul&gt; &lt;li&gt;[Doc]: Fix missing &lt;code&gt;xesmf&lt;/code&gt; APIs and update slides in intro notebook by @tomvothecoder in &lt;a href="https://github.com/xCDAT/xcdat/pull/428"&gt;https://github.com/xCDAT/xcdat/pull/428&lt;/a&gt;&lt;/li&gt; &lt;li&gt;Raise warning if no time coords found with &lt;code&gt;decode_times&lt;/code&gt; by @tomvothecoder in &lt;a href="https://github.com/xCDAT/xcdat/pull/409"&gt;https://github.com/xCDAT/xcdat/pull/409&lt;/a&gt;&lt;/li&gt; &lt;li&gt;Bump conda env dependencies by @tomvothecoder in &lt;a href="https://github.com/xCDAT/xcdat/pull/408"&gt;https://github.com/xCDAT/xcdat/pull/408&lt;/a&gt;&lt;/li&gt; &lt;li&gt;Fix &lt;code&gt;swap_lon_axis()&lt;/code&gt; breaking when sorting with singleton coords by @tomvothecoder in &lt;a href="https://github.com/xCDAT/xcdat/pull/392"&gt;https://github.com/xCDAT/xcdat/pull/392&lt;/a&gt;&lt;/li&gt; &lt;/ul&gt; &lt;p&gt;Documentation&lt;/p&gt; &lt;ul&gt; &lt;li&gt;Bump to v0.5.0 by @tomvothecoder in &lt;a href="https://github.com/xCDAT/xcdat/pull/436"&gt;https://github.com/xCDAT/xcdat/pull/436&lt;/a&gt;&lt;/li&gt; &lt;li&gt;Update xsearch-xcdat-example.ipynb by @pochedls in &lt;a href="https://github.com/xCDAT/xcdat/pull/425"&gt;https://github.com/xCDAT/xcdat/pull/425&lt;/a&gt;&lt;/li&gt; &lt;li&gt;Updates xesmf docs by @jasonb5 in &lt;a href="https://github.com/xCDAT/xcdat/pull/432"&gt;https://github.com/xCDAT/xcdat/pull/432&lt;/a&gt;&lt;/li&gt; &lt;li&gt;[Doc]: Fix missing &lt;code&gt;xesmf&lt;/code&gt; APIs and update slides in intro notebook by @tomvothecoder in &lt;a href="https://github.com/xCDAT/xcdat/pull/428"&gt;https://github.com/xCDAT/xcdat/pull/428&lt;/a&gt;&lt;/li&gt; &lt;li&gt;Add presentations and demos to sphinx toctree by @tomvothecoder in &lt;a href="https://github.com/xCDAT/xcdat/pull/422"&gt;https://github.com/xCDAT/xcdat/pull/422&lt;/a&gt;&lt;/li&gt; &lt;li&gt;[Doc]: Add &lt;code&gt;xsearch&lt;/code&gt; demo notebook for CWSS Presentation by @tomvothecoder in &lt;a href="https://github.com/xCDAT/xcdat/pull/398"&gt;https://github.com/xCDAT/xcdat/pull/398&lt;/a&gt;&lt;/li&gt; &lt;li&gt;Update temporal &lt;code&gt;.average&lt;/code&gt; and &lt;code&gt;.departures&lt;/code&gt; docstrings by @tomvothecoder in &lt;a href="https://github.com/xCDAT/xcdat/pull/407"&gt;https://github.com/xCDAT/xcdat/pull/407&lt;/a&gt;&lt;/li&gt; &lt;/ul&gt; &lt;p&gt;DevOps&lt;/p&gt; &lt;ul&gt; &lt;li&gt;Bump conda env dependencies by @tomvothecoder in &lt;a href="https://github.com/xCDAT/xcdat/pull/408"&gt;https://github.com/xCDAT/xcdat/pull/408&lt;/a&gt;&lt;/li&gt; &lt;/ul&gt; &lt;p&gt;&lt;strong&gt;Full Changelog&lt;/strong&gt;: &lt;a href="https://github.com/xCDAT/xcdat/compare/v0.4.0...0.5.0"&gt;https://github.com/xCDAT/xcdat/compare/v0.4.0...0.5.0&lt;/a&gt;&lt;/p&gt

xCDAT/xcdat: v0.6.0rc1

&lt;p&gt;v0.6.0rc1 (7 July 2023)&lt;/p&gt; &lt;p&gt;This is the first release candidate for the upcoming v0.6.0 release. This version is intended to be used for testing new features, improvements, and bug fixes. Refer to the changelog below for more information.&lt;/p&gt; &lt;p&gt;Features&lt;/p&gt; &lt;ul&gt; &lt;li&gt;Functions to produce accurate time bounds by @pochedls in &lt;a href="https://github.com/xCDAT/xcdat/pull/418"&gt;https://github.com/xCDAT/xcdat/pull/418&lt;/a&gt;&lt;/li&gt; &lt;li&gt;Add API extending xgcm vertical regridding by @jasonb5 in &lt;a href="https://github.com/xCDAT/xcdat/pull/388"&gt;https://github.com/xCDAT/xcdat/pull/388&lt;/a&gt;&lt;/li&gt; &lt;li&gt;Update &lt;code&gt;create_grid&lt;/code&gt; args to improve usability by @jasonb5 in &lt;a href="https://github.com/xCDAT/xcdat/pull/507"&gt;https://github.com/xCDAT/xcdat/pull/507&lt;/a&gt;&lt;/li&gt; &lt;/ul&gt; &lt;p&gt;Bug Fixes&lt;/p&gt; &lt;ul&gt; &lt;li&gt;Improves error when axis is missing/incorrect attributes by @jasonb5 in &lt;a href="https://github.com/xCDAT/xcdat/pull/481"&gt;https://github.com/xCDAT/xcdat/pull/481&lt;/a&gt;&lt;/li&gt; &lt;li&gt;Fix multi-file dataset spatial average orientation and weights when lon bounds span prime meridian by @pochedls in &lt;a href="https://github.com/xCDAT/xcdat/pull/495"&gt;https://github.com/xCDAT/xcdat/pull/495&lt;/a&gt;&lt;/li&gt; &lt;li&gt;Fixes preserving ds/da attributes in the regrid2 module by @jasonb5 in &lt;a href="https://github.com/xCDAT/xcdat/pull/468"&gt;https://github.com/xCDAT/xcdat/pull/468&lt;/a&gt;&lt;/li&gt; &lt;/ul&gt; &lt;p&gt;Deprecations&lt;/p&gt; &lt;ul&gt; &lt;li&gt;Add deprecation warning for CDML/XML support in &lt;code&gt;open_mfdataset()&lt;/code&gt; by @tomvothecoder in &lt;a href="https://github.com/xCDAT/xcdat/pull/503"&gt;https://github.com/xCDAT/xcdat/pull/503&lt;/a&gt;&lt;/li&gt; &lt;/ul&gt; &lt;p&gt;Documentation&lt;/p&gt; &lt;ul&gt; &lt;li&gt;Typo fix for doc by @lee1043 in &lt;a href="https://github.com/xCDAT/xcdat/pull/491"&gt;https://github.com/xCDAT/xcdat/pull/491&lt;/a&gt;&lt;/li&gt; &lt;li&gt;Update documentation in regrid2.py by @lee1043 in &lt;a href="https://github.com/xCDAT/xcdat/pull/509"&gt;https://github.com/xCDAT/xcdat/pull/509&lt;/a&gt;&lt;/li&gt; &lt;li&gt;Remove cdms-filemap references in API docstrings by @tomvothecoder in &lt;a href="https://github.com/xCDAT/xcdat/pull/504"&gt;https://github.com/xCDAT/xcdat/pull/504&lt;/a&gt;&lt;/li&gt; &lt;li&gt;Add more fields to GH Discussions question form by @tomvothecoder in &lt;a href="https://github.com/xCDAT/xcdat/pull/480"&gt;https://github.com/xCDAT/xcdat/pull/480&lt;/a&gt;&lt;/li&gt; &lt;li&gt;Add Q&amp;A GH discussions template by @tomvothecoder in &lt;a href="https://github.com/xCDAT/xcdat/pull/479"&gt;https://github.com/xCDAT/xcdat/pull/479&lt;/a&gt;&lt;/li&gt; &lt;li&gt;Update FAQs question covering datasets with conflicting bounds by @tomvothecoder in &lt;a href="https://github.com/xCDAT/xcdat/pull/474"&gt;https://github.com/xCDAT/xcdat/pull/474&lt;/a&gt;&lt;/li&gt; &lt;li&gt;Functions to produce accurate time bounds by @pochedls in &lt;a href="https://github.com/xCDAT/xcdat/pull/418"&gt;https://github.com/xCDAT/xcdat/pull/418&lt;/a&gt;&lt;/li&gt; &lt;li&gt;Add Google Groups mailing list to docs by @tomvothecoder in &lt;a href="https://github.com/xCDAT/xcdat/pull/452"&gt;https://github.com/xCDAT/xcdat/pull/452&lt;/a&gt;&lt;/li&gt; &lt;li&gt;Fix README link to CODE-OF-CONDUCT.rst by @tomvothecoder in &lt;a href="https://github.com/xCDAT/xcdat/pull/444"&gt;https://github.com/xCDAT/xcdat/pull/444&lt;/a&gt;&lt;/li&gt; &lt;li&gt;Replace LLNL E3SM License with xCDAT License by @tomvothecoder in &lt;a href="https://github.com/xCDAT/xcdat/pull/443"&gt;https://github.com/xCDAT/xcdat/pull/443&lt;/a&gt;&lt;/li&gt; &lt;/ul&gt; &lt;p&gt;DevOps&lt;/p&gt; &lt;ul&gt; &lt;li&gt;Fix Python deprecation comment in conda env yml files by @tomvothecoder in &lt;a href="https://github.com/xCDAT/xcdat/pull/514"&gt;https://github.com/xCDAT/xcdat/pull/514&lt;/a&gt;&lt;/li&gt; &lt;li&gt;Simplify conda environments and move configs to &lt;code&gt;pyproject.toml&lt;/code&gt; by @tomvothecoder in &lt;a href="https://github.com/xCDAT/xcdat/pull/512"&gt;https://github.com/xCDAT/xcdat/pull/512&lt;/a&gt;&lt;/li&gt; &lt;li&gt;Update DevOps to cache conda and fix attributes not being preserved with &lt;code&gt;xarray &gt; 2023.3.0&lt;/code&gt; by @tomvothecoder in &lt;a href="https://github.com/xCDAT/xcdat/pull/465"&gt;https://github.com/xCDAT/xcdat/pull/465&lt;/a&gt;&lt;/li&gt; &lt;li&gt;Update GH Actions to use &lt;code&gt;mamba&lt;/code&gt; by @tomvothecoder in &lt;a href="https://github.com/xCDAT/xcdat/pull/450"&gt;https://github.com/xCDAT/xcdat/pull/450&lt;/a&gt;&lt;/li&gt; &lt;li&gt;Bump to 0.6.0rc1 by @tomvothecoder in &lt;a href="https://github.com/xCDAT/xcdat/pull/515"&gt;https://github.com/xCDAT/xcdat/pull/515&lt;/a&gt;&lt;/li&gt; &lt;/ul&gt; &lt;p&gt;&lt;strong&gt;Full Changelog&lt;/strong&gt;: &lt;a href="https://github.com/xCDAT/xcdat/compare/v0.5.0...v0.6.0rc1"&gt;https://github.com/xCDAT/xcdat/compare/v0.5.0...v0.6.0rc1&lt;/a&gt;&lt;/p&gt

xCDAT/xcdat: v0.3.3

&lt;p&gt;v0.3.3 (12 October 2022)&lt;/p&gt; &lt;p&gt;This patch release fixes a bug where calculating daily climatologies/departures for specific CF calendar types that have leap days breaks when using &lt;code&gt;cftime&lt;/code&gt;. It also includes documentation updates.&lt;/p&gt; &lt;p&gt;Bug Fixes&lt;/p&gt; &lt;ul&gt; &lt;li&gt;Drop leap days based on CF calendar type to calculate daily climatologies and departures by @tomvothecoder and @lee1043 in &lt;a href="https://github.com/xCDAT/xcdat/pull/350"&gt;https://github.com/xCDAT/xcdat/pull/350&lt;/a&gt; &lt;ul&gt; &lt;li&gt;Affected CF calendar types include &lt;code&gt;gregorian&lt;/code&gt;, &lt;code&gt;proleptic_gregorian&lt;/code&gt;, and &lt;code&gt;standard&lt;/code&gt; &lt;ul&gt; &lt;li&gt;Since a solution implementation for handling leap days is generally opinionated, we decided to go with the route of least complexity and overhead (drop the leap days before calculations). We may revisit adding more options for the user to determine how they want to handle leap days (based on how valuable/desired it is).&lt;/li&gt; &lt;/ul&gt; &lt;/li&gt; &lt;/ul&gt; &lt;/li&gt; &lt;/ul&gt; &lt;p&gt;Documentation&lt;/p&gt; &lt;ul&gt; &lt;li&gt;Add horizontal regridding gallery notebook by @jasonb5 in &lt;a href="https://github.com/xCDAT/xcdat/pull/328"&gt;https://github.com/xCDAT/xcdat/pull/328&lt;/a&gt;&lt;/li&gt; &lt;li&gt;Add doc for staying up to date with releases by @tomvothecoder in &lt;a href="https://github.com/xCDAT/xcdat/pull/355"&gt;https://github.com/xCDAT/xcdat/pull/355&lt;/a&gt;&lt;/li&gt; &lt;/ul&gt; &lt;p&gt;Dependencies&lt;/p&gt; &lt;ul&gt; &lt;li&gt;&lt;code&gt;xarray &gt;= 0.21.0&lt;/code&gt; is the new constraint in the &lt;a href="https://github.com/conda-forge/xcdat-feedstock/blob/5077ec26bf9efdadbb09fc71ef3efec72e722a9c/recipe/meta.yaml#L31"&gt;conda-forge recipe&lt;/a&gt;. &lt;ul&gt; &lt;li&gt;xcdat uses &lt;a href="https://github.com/xCDAT/xcdat/blob/36a3539db2b8e5d906d6afa741c7a5908025061a/xcdat/dataset.py#L13"&gt;xarray.coding.times&lt;/a&gt;, which is only available in &lt;code&gt;xarray &gt;= 0.21.0&lt;/code&gt;.&lt;/li&gt; &lt;/ul&gt; &lt;/li&gt; &lt;/ul&gt; &lt;p&gt;&lt;strong&gt;Full Changelog&lt;/strong&gt;: &lt;a href="https://github.com/xCDAT/xcdat/compare/v0.3.2...v0.3.3"&gt;https://github.com/xCDAT/xcdat/compare/v0.3.2...v0.3.3&lt;/a&gt;&lt;/p&gt

PCMDI/pcmdi_metrics: PMP Version 2.1.1

Self contained packages to run PCMDI Metric

xCDAT/xcdat: v0.6.0

v0.6.0 (10 October 2023) This minor version update consists of new features including vertical regridding (extension of xgcm), functions for producing accurate time bounds, and improving the usability of the create_grid API. It also includes bug fixes to preserve attributes when using regrid2 horizontal regridder and fixing multi-file datasets spatial average orientation and weights when lon bounds span prime meridian. Features Functions to produce accurate time bounds by @pochedls in https://github.com/xCDAT/xcdat/pull/418 Add API extending xgcm vertical regridding by @jasonb5 in https://github.com/xCDAT/xcdat/pull/388, https://github.com/xCDAT/xcdat/pull/535, https://github.com/xCDAT/xcdat/pull/525 Update create_grid args to improve usability by @jasonb5 in https://github.com/xCDAT/xcdat/pull/507, https://github.com/xCDAT/xcdat/pull/539 Deprecation Add deprecation warnings for add_bounds boolean args by @tomvothecoder in https://github.com/xCDAT/xcdat/pull/548, Add deprecation warning for CDML/XML support in open_mfdataset() by @tomvothecoder in https://github.com/xCDAT/xcdat/pull/503, https://github.com/xCDAT/xcdat/pull/504 Bug Fixes Horizontal Regridding Improves error when axis is missing/incorrect attributes with regrid2 by @jasonb5 in https://github.com/xCDAT/xcdat/pull/481 Fixes preserving ds/da attributes in the regrid2 module by @jasonb5 in https://github.com/xCDAT/xcdat/pull/468 Fixes duplicate parameter in regrid2 docs by @jasonb5 in https://github.com/xCDAT/xcdat/pull/532 Spatial Averaging Fix multi-file dataset spatial average orientation and weights when lon bounds span prime meridian by @pochedls in https://github.com/xCDAT/xcdat/pull/495 Documentation Typo fix for climatology code example in docs by @lee1043 in https://github.com/xCDAT/xcdat/pull/491 Update documentation in regrid2.py by @lee1043 in https://github.com/xCDAT/xcdat/pull/509 Add more fields to GH Discussions question form by @tomvothecoder in https://github.com/xCDAT/xcdat/pull/480 Add Q&A GH discussions template by @tomvothecoder in https://github.com/xCDAT/xcdat/pull/479 Update FAQs question covering datasets with conflicting bounds by @tomvothecoder in https://github.com/xCDAT/xcdat/pull/474 Add Google Groups mailing list to docs by @tomvothecoder in https://github.com/xCDAT/xcdat/pull/452 Fix README link to CODE-OF-CONDUCT.rst by @tomvothecoder in https://github.com/xCDAT/xcdat/pull/444 Replace LLNL E3SM License with xCDAT License by @tomvothecoder in https://github.com/xCDAT/xcdat/pull/443 Update getting started and HPC documentation by @tomvothecoder in https://github.com/xCDAT/xcdat/pull/553 DevOps Fix Python deprecation comment in conda env yml files by @tomvothecoder in https://github.com/xCDAT/xcdat/pull/514 Simplify conda environments and move configs to pyproject.toml by @tomvothecoder in https://github.com/xCDAT/xcdat/pull/512 Update DevOps to cache conda and fix attributes not being preserved with xarray > 2023.3.0 by @tomvothecoder in https://github.com/xCDAT/xcdat/pull/465 Update GH Actions to use mamba by @tomvothecoder in https://github.com/xCDAT/xcdat/pull/450 Update constraint cf_xarray >=0.7.3 to workaround xarray import issue by @tomvothecoder in https://github.com/xCDAT/xcdat/pull/547 Full Changelog: https://github.com/xCDAT/xcdat/compare/v0.5.0...v0.6.