Python package changelog

0.2.1

• The package draws with version 0.3.11 of the geneviewer JavaScript library, with the fixes for empty charts, hidden labels and tooltips below.
• normalize() spaces the genes over the whole span of their cluster, as documented. It shared the total gap between as many gaps as there are genes, one too many, so every gap was too small and the cluster ended before its last gene did: genes at 10-40, 90-120 and 130-160 became 10-40, 60-90 and 110-140, and are now 10-40, 70-100 and 130-160. Genes that are already evenly spaced stay where they are, and a given gap is the gap drawn; it was (n - 1) / n of it for n genes. Charts made with normalize() change. The R package has the same fix.
• links(group=) works on data with a column named cluster when the clusters of the chart are another column, e.g. GC(data, cluster="genome"); it stopped with "cannot reindex on an axis with duplicate labels". That column is left out of the links. Links by that column itself (group="cluster") stop with a message to rename it.
• read_fasta() gives every sequence with a location a strand, also in files whose locations are all forward. Before, such a file had no strand column, and in a folder with other files its rows got None, which GC(strand="strand") rejects.
• read_gff() and read_bed() give the column types of the R package 0.2.1, so the files of a folder can be combined when a column holds numbers in one file and text in another (e.g. chromosomes 1 and X). seqid, source, type, strand and phase of GFF files, and chrom, name, strand and itemRgb of BED files are always text; score is always numbers, NaN for a score of ".". A score that is not a number becomes NaN, with a warning.
• Links made with links(group=) before normalize() move with their genes; they stayed at the old positions. Links given as data (e.g. alignments) keep their positions, with a warning to add them after normalize().
• read_bed() reads files whose columns are separated by spaces (in a file without any tab), and names columns after the twelve of BED V13, V14, ... (the 13th was NA.).
• read_fasta() on a folder without FASTA files stops with "No .fasta files found in the specified directory.", as the other readers; it gave an empty table.
• get_introns() (and transcript()): an intron keeps the columns that are the same for all exons and UTRs of its transcript and is missing the others. It copied the exon before it, so a label of each exon, e.g. labels("exon_id"), was repeated on the intron after it.
• Clearer errors for wrong arguments: grid(margin=) takes pixels or a percentage of a chart height in pixels; legend(group=) one column; scale(scale_breaks=) and links(measure=) one value; links(value1=, value2=) both or neither, of the same length (a missing value2 was ignored without a message).
• cluster(separate_strands=True, prevent_gene_overlap=True) warns that neither is applied, which is what happens; it said "Resetting to None". The docs of grid() say what a width number is (pixels).
• Tooltips (tooltip()) show the values of the data as text: markup in a value, e.g. in a qualifier of a GenBank file from someone else, ran in the page of who viewed the chart. The formatter is still HTML.
• mummer_alignment() reads a folder whose path has spaces: the files are copied to a working folder in output_dir first, so only that path must be without spaces.
• zoom(range=) and zoom(min=) are checked in the mode of an earlier zoom() when the call gives none: .zoom(mode="absolute").zoom(range=[100, 2000]) stopped with the error for a relative range.
• show=False in labels(), coordinates(), scale_bar(), cluster_title(), cluster_label() and cluster_footer() hides what an earlier call shows, e.g. .coordinates().coordinates(show=False, cluster=2); it changed nothing. Hidden labels need no label column. With nothing shown before, the chart is unchanged, as before.
• A chart of data without rows (or only rows without a start or end) takes the chart's methods: labels("name") and legend() stopped with "column not found in data", and normalize() and transcript() with an internal error. The chart has no clusters and draws as an empty chart.
• genbank_to_fasta() writes records without a VERSION line, named by their ACCESSION, else their LOCUS name, else the file name; without a DEFINITION, the header is the name only. They were left out without a message, so the FASTA file could be empty.
• read_gbk() reads features whose key does not start with a letter, such as 5'UTR, 3'UTR and -10_signal; their lines were added to the feature before them. Qualifiers without a value, such as /pseudo, are kept, with the value "", and a feature without qualifiers gets its region.
• read_gbk() reads the whole sequence (ORIGIN) of records of more than a million bases; it stopped at base 1,000,020, without a message.

0.2.0

• Charts in Jupyter notebooks, with the new jupyter extra (pip install "geneviewer-py[jupyter]"): a cell that ends with a chart draws it. It works where anywidget does: JupyterLab, Jupyter Notebook, VS Code, Google Colab and marimo.
• chart.widget() gives the chart as a widget (geneviewer.jupyter.GCWidget) to keep in a variable. Its attributes hold the chart's events, as the inputs of a Shiny app do (widget.select, widget.zoom, ...), widget.on("select", callback) calls a function at each event, widget.zoom_to() moves the zoom slider, and setting widget.chart draws another chart in the same place.

0.1.0

The first release: the charts of the geneviewer R package and JavaScript library from Python, in Shiny for Python.

• GC() makes a chart from a pandas DataFrame of genes, or from a GenBank file or folder. Its methods are the GC_ functions of the R package (.labels(), .links(), .transcript(), .theme(), ...), with the same arguments in snake_case. A chart in Python and one in R with the same arguments give the same chart.
• geneviewer.shiny: output_geneviewer() and @render_geneviewer show a chart in a Shiny for Python app, its events are inputs such as input.chart_select(), and zoom_to() moves the zoom slider from the server.
• File readers: read_gbk(), gbk_features_to_df(), read_gff(), read_fasta(), read_bed() and genbank_to_fasta(), with the results of the R package's readers.
• Alignment: protein_blast() (with the align extra) and mummer_alignment() (with MUMmer installed).
• geneviewer.datasets: the 11 example datasets of the R package.
• geneviewer_theme() and geneviewer_palette() give the settings of the built-in themes and the colours of the palettes.

The package draws with version 0.3.10 of the geneviewer JavaScript library, which it includes.