From 99d0ef76f85f64659388c219e639c47324e7f213 Mon Sep 17 00:00:00 2001 From: Saket Choudhary Date: Sun, 17 Sep 2023 12:18:24 -0400 Subject: [PATCH] Update HISTORY.md --- HISTORY.md | 124 +++++++++++++++++++++++------------------------------ 1 file changed, 53 insertions(+), 71 deletions(-) diff --git a/HISTORY.md b/HISTORY.md index 5d537223..71d5aa70 100644 --- a/HISTORY.md +++ b/HISTORY.md @@ -8,30 +8,23 @@ ## 2.1.0 (2023-05-16) -- Fix for [gse-to-srp]{.title-ref} returning unrequested GSEs ([#186 - \]{.title-ref}) -- Fix for [download]{.title-ref} using [public_urls]{.title-ref} -- Fix for [gsm-to-srx]{.title-ref} returning false positives ([#165 - \]{.title-ref}) +- Fix for [gse-to-srp] returning unrequested GSEs [#186](https://github.com/saketkc/pysradb/issues/190) +- Fix for [download] using [public_urls] +- Fix for [gsm-to-srx] returning false positives [#165](https://github.com/saketkc/pysradb/issues/165) - Fix for delimiter not being consistent when metadata is printed on - terminal ([#147 - \]{.title-ref}) + terminal [#147](https://github.com/saketkc/pysradb/issues/147) - ENA search is currently broken because of an API change ## 2.0.2 (2023-04-09) -- Fix for [gse-to-srp]{.title-ref} to handle cases where a project is - missing but SRXs are returned ([#186 - \]{.title-ref}) -- Fix gse-to-gsm ([#187 - \]{.title-ref}) +- Fix for [gse-to-srp] to handle cases where a project is + missing but SRXs are returned [#186](https://github.com/saketkc/pysradb/issues/186) +- Fix gse-to-gsm [#187](https://github.com/saketkc/pysradb/issues/187) ## 2.0.1 (2023-03-18) -- Fix for [pysradb download]{.title-ref} - using - [public_url]{.title-ref} -- Fix for SRX -\> SRR and related conversions ([#183 - \]{.title-ref}) +- Fix for [pysradb download] - using [public_url] +- Fix for SRX -\> SRR and related conversions [#183](https://github.com/saketkc/pysradb/pull/183) ## 2.0.0 (2023-02-23) @@ -39,51 +32,45 @@ returned (not backward compatible); all column names are lower cased by default - Fix extra space in \"organism_taxid\" column -- Added support for Experiment attributes ([#89 - \]{.title-ref}) +- Added support for Experiment attributes [#89](https://github.com/saketkc/pysradb/issues/89#issuecomment-1439319532) ## 1.4.2 (06-17-2022) -- Fix ENA fastq fetching ([#163 - \]{.title-ref}) +- Fix ENA fastq fetching [#163](https://github.com/saketkc/pysradb/issues/163) ## 1.4.1 (06-04-2022) -- Fix for fetchin alternative URLs +- Fix for fetching alternative URLs ## 1.4.0 (06-04-2022) - Added ability to fetch alternative URLs (GCP/AWS) for metadata - ([#161 - \]{.title-ref}) -- Fix for xmldict 0.13.0 no longer defaulting to OrderedDict ([#159 - \]{.title-ref}) -- Fix for missing experiment model and description in metadata ([#160 - \]{.title-ref}) + [#161](https://github.com/saketkc/pysradb/issues/161) +- Fix for xmldict 0.13.0 no longer defaulting to OrderedDict [#159](https://github.com/saketkc/pysradb/pull/159) +- Fix for missing experiment model and description in metadata [#160](https://github.com/saketkc/pysradb/issues/160) ## 1.3.0 (02-18-2022) -- Add [study_title]{.title-ref} to [\--detailed]{.title-ref} flag +- Add [study_title] to [\--detailed] flag ([#152](https://github.com/saketkc/pysradb/issues/152)) -- Fix [KeyError]{.title-ref} in [metadata]{.title-ref} where some new +- Fix [KeyError] in [metadata] where some new IDs do not have any metadata ([#151](https://github.com/saketkc/pysradb/issues/151)) ## 1.2.0 (01-10-2022) -- Do not exit if a qeury returns no hits ([#149 - \]{.title-ref}) +- Do not exit if a qeury returns no hits ([#149](https://github.com/saketkc/pysradb/pull/149)) ## 1.1.0 (12-12-2021) -- Fixed [gsm-to-gse]{.title-ref} failure +- Fixed [gsm-to-gse] failure ([#128](https://github.com/saketkc/pysradb/pull/128)) - Fixed case sensitivity bug for ENA search ([#144](https://github.com/saketkc/pysradb/pull/144)) - Fixed publication date bug for search ([#146](https://github.com/saketkc/pysradb/pull/146)) - Added support for downloading data from GEO [pysradb dowload -g - \]{.title-ref} + GSE] ([#129](https://github.com/saketkc/pysradb/pull/129)) ## 1.0.1 (01-10-2021) @@ -96,16 +83,16 @@ defaults to `SRAweb` - `SRAweb` now supports [search](https://saket-choudhary.me/pysradb/quickstart.html#search) -- [N/A]{.title-ref} is now replaced with [pd.NA]{.title-ref} -- Two new fields in \`\--detailed\`: [instrument_model]{.title-ref} - and [instrument_model_desc]{.title-ref} +- [N/A] is now replaced with [pd.NA] +- Two new fields in \`\--detailed\`: [instrument_model] + and [instrument_model_desc] [#75](https://github.com/saketkc/pysradb/issues/75) - Updated documentation ## 0.11.1 (09-18-2020) -- [library_layout]{.title-ref} is now outputted in metadata #56 -- [-detailed]{.title-ref} unifies columns for ENA fastq links instead +- [library_layout] is now outputted in metadata #56 +- [-detailed] unifies columns for ENA fastq links instead of appending \_x/\_y #59 - bugfix for parsing namespace in xml outputs #65 - XML errors from NCBI are now handled more gracefully #69 @@ -113,9 +100,9 @@ ## 0.11.0 (09-04-2020) -- [pysradb download]{.title-ref} now supports multiple threads for +- [pysradb download] now supports multiple threads for paralle downloads -- [pysradb download]{.title-ref} also supports ultra fast downloads of +- [pysradb download] also supports ultra fast downloads of FASTQs from ENA using aspera-client ## 0.10.3 (03-26-2020) @@ -134,7 +121,7 @@ Contributors - Bug fix: Handle API-rate limit exceeding =\> Retries - Enhancement: \'Alternatives\' URLs are now part of - [\--detailed]{.title-ref} + [\--detailed] ## 0.10.1 (02-04-2020) @@ -163,7 +150,7 @@ Contributors ## 0.9.6 (07-20-2019) -- Introduced [SRAweb]{.title-ref} to perform queries over the web if +- Introduced [SRAweb] to perform queries over the web if the SQLite is missing or does not contain the relevant record. ## 0.9.0 (02-27-2019) @@ -171,7 +158,7 @@ Contributors ### Others - This release completely changes the command line interface replacing - click with argparse () + click with argparse ([#3](https://github.com/saketkc/pysradb/pull/3)) - Removed Python 2 comptaible stale code ## 0.8.0 (02-26-2019) @@ -190,7 +177,7 @@ Contributors ### Others -- [\--out_dir]{.title-ref} is now [out-dir]{.title-ref} +- [\--out_dir] is now [out-dir] ## 0.7.1 (02-18-2019) @@ -215,20 +202,20 @@ Python3. The following commad line options have been renamed and the changes are not compatible with 0.6.0 release: -- [sra-metadata]{.title-ref} -\> [metadata]{.title-ref}. -- [sra-search]{.title-ref} -\> [search]{.title-ref}. -- [srametadb]{.title-ref} -\> [metadb]{.title-ref}. +- [sra-metadata] -\> [metadata]. +- [sra-search] -\> [search]. +- [srametadb] -\> [metadb]. ## 0.6.0 (12-25-2018) ### Bugfix - Fixed bugs introduced in 0.5.0 with API changes where multiple - redundant columns were output in [sra-metadata]{.title-ref} + redundant columns were output in [sra-metadata] ### New methods/functionality -- [download]{.title-ref} now allows piped inputs +- [download] now allows piped inputs ## 0.5.0 (12-24-2018) @@ -237,9 +224,9 @@ not compatible with 0.6.0 release: - Support for filtering by SRX Id for SRA downloads. - \`srr_to_srx\`: Convert SRR to SRX/SRP - \`srp_to_srx\`: Convert SRP to SRX -- Stripped down [sra-metadata]{.title-ref} to give minimal information -- Added [\--assay]{.title-ref}, [\--desc]{.title-ref}, - [\--detailed]{.title-ref} flag for [sra-metadata]{.title-ref} +- Stripped down [sra-metadata] to give minimal information +- Added [\--assay], [\--desc], + [\--detailed] flag for [sra-metadata] - Improved table printing on terminal ## 0.4.2 (12-16-2018) @@ -252,7 +239,7 @@ not compatible with 0.6.0 release: ### New methods/functionality -- Added a new [BASEdb]{.title-ref} class to handle common database +- Added a new [BASEdb] class to handle common database connections - Initial support for GEOmetadb through GEOdb class - Initial support or a command line interface: @@ -267,20 +254,20 @@ not compatible with 0.6.0 release: ### New methods/functionality -- [sample_attribute]{.title-ref} and - [experiment_attribute]{.title-ref} are now included by default in - the df returned by [sra_metadata()]{.title-ref} +- [sample_attribute] and + [experiment_attribute] are now included by default in + the df returned by [sra_metadata()] - [expand_sample_attribute_columns: expand metadata dataframe based on - attributes in \`sample_attribute]{.title-ref} column + attributes in \`sample_attribute] column - New methods to guess cell/tissue/strain: - [guess_cell_type()]{.title-ref}/[guess_tissue_type()]{.title-ref}/[guess_strain_type()]{.title-ref} + [guess_cell_type()]/[guess_tissue_type()]/[guess_strain_type()] - Improved README and usage instructions ## 0.2.2 (12-03-2018) ### New methods/functionality -- [search_sra()]{.title-ref} allows full text search on SRA metadata. +- [search_sra()] allows full text search on SRA metadata. ## 0.2.0 (12-03-2018) @@ -289,26 +276,21 @@ not compatible with 0.6.0 release: The following methods have been renamed and the changes are not compatible with 0.1.0 release: -- [get_query()]{.title-ref} -\> [query()]{.title-ref}. -- [sra_convert()]{.title-ref} -\> [sra_metadata()]{.title-ref}. -- [get_table_counts()]{.title-ref} -\> [all_row_counts()]{.title-ref}. +- [get_query()] -\> [query()]. +- [sra_convert()] -\> [sra_metadata()]. +- [get_table_counts()] -\> [all_row_counts()]. ### New methods/functionality -- [download_sradb_file()]{.title-ref} makes fetching - [SRAmetadb.sqlite]{.title-ref} file easy; wget is no longer - required. -- [ftp]{.title-ref} protocol is now supported besides - [fsp]{.title-ref} and hence [aspera-client]{.title-ref} is now - optional. We however, strongly recommend [aspera-client]{.title-ref} - for faster downloads. +- [download_sradb_file()] makes fetching [SRAmetadb.sqlite] file easy; wget is no longer required. +- [ftp] protocol is now supported besides [fsp] and hence [aspera-client] is now optional. We however, strongly recommend [aspera-client] for faster downloads. ### Bug fixes -- Silenced [SettingWithCopyWarning]{.title-ref} by excplicitly doing +- Silenced [SettingWithCopyWarning] by excplicitly doing operations on a copy of the dataframe instead of the original. -Besides these, all methods now follow a [numpydoc]{.title-ref} +Besides these, all methods now follow a [numpydoc] compatible documentation. ## 0.1.0 (12-01-2018)