CHANGELOG.md

Changelog

All notable changes to this project will be documented in this file.

The format is based on Keep a Changelog and this project adheres to Semantic Versioning.

Unreleased

2.1.1.post2 - 2021-11-23

Fixed

• Interface break when requesting all probe candidates.

2.1.1.post1 - 2021-11-23

Fixed

• Now using version flag from importlib.

2.1.1 - 2021-11-23

Fixed

• Output directory error via GUI due to changed CLI hook call structure after switching from argparse to click.

2.1.0.post1 - 2021-10-20

Fixed

• Trove classifiers in pyproject.toml.

2.1.0 - 2021-10-20

Added

• Pre-commit hooks.

Changed

• Import of custom routes script with importlib.util.
• Updated dependencies.
• Dropped support for Python 3.6.

Fixed

• Typo in GUI via ifpd serve.
• Typos in GUI.
• Alternative tab switcher of probe-design GUI.

2.0.5 - 2021-02-22

Added

• poetry.lock file for common dependency versions.
• Logging commands submitted to queue via ifpd serve.

Changed

• Upgraded dependencies to latest versions and tested.

Fixed

• Minor bug in ifpd_mkdb triggered by databases with 1 oligo in a feature. (unlikely scenario)
• Bug in ifpd_serve that added quotes around --region start end and caused queries to fail.

2.0.4 - 2021-02-11

Added

• Tooltip to GUI explaining that setting start and end to the same value triggers a query of the whole feature.
• const.py module with package version tag and other constants.
• Option to hide breadcrumbs when running serve.
• Enforcing GUI to be accessed at serving URI, not viewing one.

Changed

• Switched from setup.py to poetry setup.
• Simplified authorship and license comment.
• Now all scripts are accessible through a single entry-point at "ifpd".
• Now asking for arguments "chrom [--region start end]" when querying.
• Single probe design default behavior now does not stop if not enough oligos are found, instead it generates a probe with the largest number of oligos. To revert to the old behavior use the --exact-n-oligo option.
• Changed extension of simple template files to .tpl.html.
• Moved documentation to docs.
• mkdb does not support sequence-less inputs anymore.
• query probe and query set argument order changed.
• Made static argument mandatory for serve, for compatibility with pipx installation.
• Error 500 now triggers a redirect to app homepage with a 5s delay.
• Breadcrumbs are on by default on serve.

Fixed

• Blacked code.
• Bugs crashing query when probe has 1 or 2 oligos only.
• Bugs crashing query when probe set has 1 or 2 probes only.

Removed

• web module and all network-based checks.
• Network-based checks from dbchk.
• Dependency from ggc and tqdm.
• Sequence-less databases due to bug.

2.0.3.post2 - 2019-09-11

Fixed

• Bug crashing web interface due to missing str2int conversion.

2.0.3.post1 - 2019-07-24

Fixed

• Bug crashing interface when no CUSTOM flags are present in a database.

2.0.3 - 2019-05-29

Added

• Option to easily add google analytics tokens to design interface.

Fixed

• Showing all probe candidates when using -1 option.

2.0.2 - 2019-02-07

Fixed

• ifpd_mkdb now does not crush at start.
  • Added --no-net option.

2.0.1.post6 - 2019-02-04

Changed

• Bootstrap grid and card layout in database tab.

Fixed

• Fixed behaviour of --list-refGenomes option.

2.0.1.post5 - 2019-02-04

Fixed

• Changed links in headers for CORS.
• Changed routes to Probe design app for "/" management.

2.0.1.post4 - 2019-02-01

Changed

• Now showing error log if a query crashes.

2.0.1.post3 - 2019-01-31

Fixed

• Calculation of oligonucleotide midpoint for plotting.

2.0.1 - 2019-01-30

Added

• Option for cookie consent banner.
• Menu advanced options.

Changed

• Moved link to close bookmark alert to the right.
• Renamed spread feature to homogeneity.
• Made fields in query form responsiv.

2.0.0.post1 - 2019-01-25

Added

• bioext module for biological file extension methods.
  • UCSCbed class to read files in UCSC bed format.
• web module for web-service related methods.
  • UCSC DAS server related methods.
• query module for query and database management.
  • Implemented oligo database class that asserts it when reading it.
• stats module for statistics-related methods.
• fprode_mkdb script: re-format a database to be compatible with FISH-ProDe.
  • List UCSC available reference genomes with --list-refGenomes.
  • .config file generated using the configparser package.
• fprode_dbchk: checks database integrity.
• Parallelization to probe set query script. (only local)

Changed

• Renamed package to ifpd.
• Moved interface documents to separate sub-folder.
• Each database is structured as follows:
  • One file per chromosome, with the name being the same as the chromosome. One row per oligo and two columns: start and end position, as per the UCSC bed format standard. Also, a third (optional) column can be present, with the sequence of the oligo.
  • One .config file with the database details.
• Database query now split in two scripts (fprode_dbquery_probe and fprode_dbquery_probeSet), for single-probe and probe-set design.
  • Query-related methods moved to the query sub-module.
  • Query ID now handled server-side, for easier standalone script execution.
  • Region of interest now passed as chrN:XXX,YYY, for convenience.
  • Query name and description now handled only server-side, i.e., removed as input parameters of the query scripts.
• Refined user interface.
• Queue in web interface now reports region and isotimestamp for each queued query.
• Queries can be reached by knowing their ID only.
• Using newer version of JavaScript libraries.

Removed

• fprode_dbextract
• Single probe batch query interface.
• Query table from interface.

1.1.0 - 2018-08-25

Changed

• Refactored as Python package.

0.0.1 - 2017-08-06 - First release