pip install or python setup.py install will now correctly copy the files in ginput/data to the installation directory. Installing in develop mode through make install is still the recommended way of setting up ginput for normal use; however, if this is part of a larger project and you want the code to live alongside your other dependencies, that works now.
Two notes:
1. ginput does cache look up tables in the data directory within the package. If you install it into your environment (rather than using develop mode), you will need to ensure that the install directory is writable by the process that will run ginput (or you disable the caching).
2. If installing with python setup.py install or pip install, it is still recommended that you use the environment-py36.yml or environment-py310.yml file to install the necessary dependencies with conda. The setup.py requirements are deliberately permissive so that it can work with either the Python 3.6 or 3.10 requirements. If you rely on pip to install the dependencies and get errors, please try to reproduce the errors in a conda environment based on the environment-py36.yml or environment-py310.yml file before opening an issue.
## What’s Changed
* Setup update for pip install by @rocheseb in https://github.com/WennbergLab/py-ginput/pull/1
Full Changelog: https://github.com/WennbergLab/py-ginput/compare/v1.1.6…v1.1.7
Public repository for the GINPUT priors generator},
year = {2022},
}
@data{10.22002/D1.20286
title = {justinbois/iqplot: 0.3.2},
author = {Justin S. Bois},
doi = {10.22002/D1.20286},
abstract = {make install or ./install.sh, a Python 3.10 conda environment is created instead of a Python 3.6 one. If you need to work with Python 3.6, the environment-py36.yml file contains the previous 3.6 environment configuration, and can be use with conda env create -f to manually create a Python 3.6 environment.
Public repository for the GINPUT priors generator},
year = {2022},
}
@data{10.22002/D1.20283
title = {justinbois/iqplot: v0.3.1},
author = {Justin S. Bois},
doi = {10.22002/D1.20283},
abstract = {Hot fix of bug involved with using swarm_kwargs in strip plots.
iqplot: Bokeh plots with one quantitative variable},
year = {2022},
}
@data{10.22002/D1.20282
title = {First steps for presentation and analysis of calcium imaging data},
author = {Andrey Andreev and Desiderio Ascencio},
doi = {10.22002/D1.20282},
abstract = {Calcium imaging is a widely used tool in neuroscience, and our community now has access to multiple computational tools to process and analyze these data. However, significant portion of work with imaging data relies on much simpler approaches than offered in these software packages. Correlation with stimuli or behavior, detection of periodic activity, dimensionality reduction, and other basic approaches can be straight-forward for researchers seasoned in data analysis, but unfamiliar to larger community of experimental neuroscientists. Here we provide examples of such analysis using Python language together with sample open-access datasets. We discuss questions addressed with standard algorithms and offer documented Jupiter notebooks ready to be adapted for other data.},
year = {2022},
}
@data{10.22002/D1.20280
title = {caltechlibrary/cell-atlas: Release 2.3},
author = {Oikonomou, Catherine and Jensen, Grant and Morrell, Thomas E},
doi = {10.22002/D1.20280},
abstract = {This release adds minor updates to the video and text content of “The Atlas of Bacterial & Archaeal Cell Structure” site, including seven new scientist profiles.
Cell atlas},
year = {2022},
}
@data{10.22002/D1.20275
title = {caltechlibrary/epxml_to_datacite: M1 support and general fixes},
author = {Morrell, Thomas E},
doi = {10.22002/D1.20275},
abstract = {This release includes M1 support for Macs, as well as a number of other bug fixes. It enhances the caltechauthors script with support for text file inputs and improvements to series and numbering information transfer. It also fixes a bug with accepted date transfer.
Full Changelog: https://github.com/caltechlibrary/epxml_to_datacite/compare/v1.1…v1.2
Transform Eprints XML to DataCite XML},
year = {2022},
}
@data{10.22002/D1.20270
title = {caltechlibrary/py-cli-template: Release 1.6.0 – misc minor fixes},
author = {Hucka, Michael and Doiel, Robert and Morrell, Thomas E. and Keswick, Tommy},
doi = {10.22002/D1.20270},
abstract = {In this release:
* Use a setup.cfg setting for py.test paths, and remove the code that munged sys.path in the test files.
* Try to use a more reliable path to the Caltech logo image.
* Remove LICENSE.html file because it confuses GitHub.
GitHub template project for non-web Python application projects.},
year = {2022},
}
@data{10.22002/D1.20257
title = {viscofric2d_evo},
author = {Mallick, Rishav},
doi = {10.22002/D1.20257},
abstract = {MATLAB code to simulate post- and inter-seismic evolution of fault velocity and strain rate in a viscoelastic channel, considering linear, power-law and linear Burger’s rheologies. The simulations are consistent over short-term as well as long-term. Code is maintained at https://github.com/mallickrishg/viscofric2d_evo},
year = {2022},
}
@data{10.22002/D1.20254
title = {caltechlibrary/foliage: Release 1.4.1},
author = {Hucka, Mike},
doi = {10.22002/D1.20254},
abstract = {Foliage is the FOLIo chAnGe Editor, a tool to do bulk changes in FOLIO using the network API.},
year = {2022},
}
@data{10.22002/D1.20247
title = {justinbois/iqplot: v. 0.3.0},
author = {Justin S. Bois},
doi = {10.22002/D1.20247},
abstract = {jitter kwarg is now replaced by spread.
- click_policy kwarg is now replaced by legend_click_policy.
- conf_int_kwargs is now replaced by fill_kwargs.
iqplot: Bokeh plots with one quantitative variable},
year = {2022},
}
@data{10.22002/D1.20246
title = {caltechlibrary/foliage: Release 1.4.0},
author = {Hucka, Mike},
doi = {10.22002/D1.20246},
abstract = {Foliage is the FOLIo chAnGe Editor, a tool to do bulk changes in FOLIO using the network API.},
year = {2022},
}
@data{10.22002/D1.20243
title = {caltechlibrary/cell-atlas: Release 2.2},
author = {Oikonomou, Catherine and Jensen, Grant and Morrell, Thomas E},
doi = {10.22002/D1.20243},
abstract = {This release adds brand new features to the “The Atlas of Bacterial & Archaeal Cell Structure” site, as well as enhancing and refactoring existing features. These updates include changes such as:
- Add feature index generation from section/subsection metadata.
- Replace previous custom video player with videojs.
- Add keyboard panning to Phylogenetic Tree and Phylogenetic tree information in list form to the tree viewer page.
Cell atlas},
year = {2022},
}
@data{10.22002/D1.20238
title = {caltechlibrary/py-cli-template: Release 1.5.0 – add starting test cases for testing CLI},
author = {Hucka, Michael and Doiel, Robert and Morrell, Thomas E. and Keswick, Tommy},
doi = {10.22002/D1.20238},
abstract = {This release adds a test file to help start testing the CLI.
GitHub template project for non-web Python application projects.},
year = {2022},
}
@data{10.22002/D1.20232
title = {Software: WormRuler: A software to track body length used to characterize a super red-shifted channelrhodopsin in Caenorhabditis elegans},
author = {Alexander Gottschalk},
doi = {10.22002/D1.20232},
abstract = {WormRuler Software
ASTNode_isLogical by @giordano in https://github.com/sbmlteam/libsbml/pull/230
* improve thread safety of UnitFormulaFormatter, PowerUnitsCheck by @lkeegan in https://github.com/sbmlteam/libsbml/pull/233
* Fix signature of SBase_getNumPlugins in prototype by @giordano in https://github.com/sbmlteam/libsbml/pull/237
* Ensure Translate/OutputSBML work on Octave and Matlab by @fbergmann in https://github.com/sbmlteam/libsbml/pull/175
* - add whitespace by @fbergmann in https://github.com/sbmlteam/libsbml/pull/239
* add FbcReactionPlugin_createGeneProductAssociation to C API by @exaexa in https://github.com/sbmlteam/libsbml/pull/247
* Cmake libxml fix by @fbergmann in https://github.com/sbmlteam/libsbml/pull/250
* Add SBMLNamespaces_addPackageNamespace{,s} functions to C API by @giordano in https://github.com/sbmlteam/libsbml/pull/235
* #241:issues with fbc v3 by @fbergmann in https://github.com/sbmlteam/libsbml/pull/243
## New Contributors
* @exaexa made their first contribution in https://github.com/sbmlteam/libsbml/pull/247
Full Changelog: https://github.com/sbmlteam/libsbml/compare/v5.19.5…v5.19.6
LibSBML is a native library for reading, writing and manipulating files and data streams containing the Systems Biology Markup Language (SBML). It offers language bindings for C, C++, C#, Java, JavaScript, MATLAB, Perl, PHP, Python, R and Ruby.
.gitignore},
author = {Hucka, Michael and Doiel, Robert and Morrell, Thomas E. and Keswick, Tommy},
doi = {10.22002/D1.20225},
abstract = {This release changes the default .gitignore contents and the recommended practices around it.
The new approach is to add only project-specific rules in the .gitignore. Rules that apply to a person’s way of doing things (and the particular tools they happen to use) should instead go into a user’s global git ignore file. For example, Emacs checkpoint and backup files are things that are not specific to a given project; rather, Emacs users will see them created everywhere, in all projects, because they’re a byproduct of using Emacs, not a consequence of working on a particular project. Thus, they belong in a user’s global ignores list, not in this project .gitignore.
.gitignore (Version v1.4.0) [Computer software]. CaltechDATA. https://doi.org/10.22002/D1.20225This version adds new new features: * The Change Records tab now supports changing the loan type on records. * A new tab, Clean Records, is available. It currently has one capability: to delete “phantom” loans based on user id’s, meaning loan records associated with users but for items that no longer exist in Folio.
Foliage is the FOLIo chAnGe Editor, a tool to do bulk changes in FOLIO using the network API.Makefile, setup.py, CITATION.cff, others. Also, added GitHub issue and PR templates, and a starting point for writing tests. The Makefile has new targets for “make tests” and “make lint”.
GitHub template project for non-web Python application projects.
The main functional change in this release is that error objects returned by net(...) will have error message bodies returned by network services, where possible.
Internally, there has been some refactoring of the Makefile and addition of things like GitHub template files.
Collection of common Python utility functions and classes used in other Caltech Library programs.