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saketkc committed Sep 17, 2023
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## 2.1.0 (2023-05-16)

- Fix for [gse-to-srp]{.title-ref} returning unrequested GSEs ([#186
\<https://github.com/saketkc/pysradb/issues/190\>]{.title-ref})
- Fix for [download]{.title-ref} using [public_urls]{.title-ref}
- Fix for [gsm-to-srx]{.title-ref} returning false positives ([#165
\<https://github.com/saketkc/pysradb/issues/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
\<https://github.com/saketkc/pysradb/issues/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
\<https://github.com/saketkc/pysradb/issues/186\>]{.title-ref})
- Fix gse-to-gsm ([#187
\<https://github.com/saketkc/pysradb/issues/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
\<https://github.com/saketkc/pysradb/pull/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)

- BREAKING change: Overhaul of how urls and associated metadata are
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
\<https://github.com/saketkc/pysradb/issues/89#issuecomment-1439319532\>]{.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
\<https://github.com/saketkc/pysradb/issues/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
\<https://github.com/saketkc/pysradb/issues/161\>]{.title-ref})
- Fix for xmldict 0.13.0 no longer defaulting to OrderedDict ([#159
\<https://github.com/saketkc/pysradb/pull/159\>]{.title-ref})
- Fix for missing experiment model and description in metadata ([#160
\<https://github.com/saketkc/pysradb/issues/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
\<https://github.com/saketkc/pysradb/pull/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
\<GSE\>]{.title-ref}
GSE]
([#129](https://github.com/saketkc/pysradb/pull/129))

## 1.0.1 (01-10-2021)
Expand All @@ -96,26 +83,26 @@
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
- Documentation and dependency updates

## 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)
Expand All @@ -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)

Expand Down Expand Up @@ -163,15 +150,15 @@ 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)

### Others

- This release completely changes the command line interface replacing
click with argparse (<https://github.com/saketkc/pysradb/pull/3>)
click with argparse ([#3](https://github.com/saketkc/pysradb/pull/3))
- Removed Python 2 comptaible stale code

## 0.8.0 (02-26-2019)
Expand All @@ -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)

Expand All @@ -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)

Expand All @@ -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)
Expand All @@ -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:
Expand All @@ -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)

Expand All @@ -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)
Expand Down

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