Merge from eyurtsev/fcsparser #3
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Add module requirements to setup.py
Added try/except statement for invalid unicode characters in heade
Update list of supported machines
Support for loading in-memory files
added bioconda recipe
* Update fromfile to support 3-byte fields Some FCS files (such as the one generated by the Cytek xP5) store integers in 3-byte fields. This breaks numpy's parser, which only wants power-of-two sized fields. So, I've updated fromfile() to parse FCS files as a table of 1-byte unsigned ints, expand those fields to 4 bytes, and then re-view them as the proper dtype. My only concern is that this may break on an FCS file produced by a big-endian machine (because I'm adding the extra bytes to the beginning of the field). I don't have ready access to any of those -- do you? * add tests for 3-byte DATA * documentation for fromfile() changes
* Update * Update
#37) * If the FCS file uses whitespace delimiters (e.g. \x0c) avoid stripping Otherwise the $BEGINDATA could be cut. In my case I had headers without 'data start' where the first data row had: \x0c$BEGINDATA So doing both the trim and the raw_text = raw_text[1:] means that we cut off the '$' which results in an error on line 381: self._data_start = int(text['$BEGINDATA']) * Added unit tests for whitespace delimiter Co-authored-by: Gergely Csegzi <gcsegzi@palantir.com>
Instead of making `cytoflow` depend on `fcsparser`, I would like to include `fcsparser` as a submodule. This way, if I have fixes that I want to roll out with a `cytoflow` release, I don't have to wait on you to roll a new release of `fcsparser`. (Making new releases is harder than it should be.) This would be a lot easier on my end if `fcsparser.__init__` used a relative import instead of an absolute import. This way, the directory containing `api.py` doesn't have to be in `sys.path`. It should not effect folks who use `fcsparser` directly.
Bumps [numpy](https://github.com/numpy/numpy) from 1.21.1 to 1.22.0. - [Release notes](https://github.com/numpy/numpy/releases) - [Changelog](https://github.com/numpy/numpy/blob/main/doc/HOWTO_RELEASE.rst) - [Commits](numpy/numpy@v1.21.1...v1.22.0) --- updated-dependencies: - dependency-name: numpy dependency-type: direct:production ... Signed-off-by: dependabot[bot] <support@github.com> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
* fix for FCS files with multiple datasets * Expand unit-tests * Add tests for multi tube file parsing to pr (#45) * resolves unittest issue with multi tube fcs parsing * adds vscode, dist, build and venv folders to .gitignore --------- Co-authored-by: Florian Kowarsch <florian.kowarsch@tuwien.ac.at> --------- Co-authored-by: Brian Teague <bpteague@gmail.com> Co-authored-by: Florian Kowarsch <39064983+CaRniFeXeR@users.noreply.github.com> Co-authored-by: Florian Kowarsch <florian.kowarsch@tuwien.ac.at>
Update workflows, update readme and manifest
See release notes for details
BD facs diva devices only have channel_name_s set for some but not all channels. If not present for all channels fcsparser fallbacks to the channel_names_n. This pull request includes two main adaptations: - Using channel_names_n as a fallback for channels without a value in channel_names_s - Puts both $PnN and $PnS as columns into the metadata dataframe All adaptations have corresponding unit tests
see release notes
Update link to documentation
Bumps [tornado](https://github.com/tornadoweb/tornado) from 6.3.1 to 6.3.3. - [Changelog](https://github.com/tornadoweb/tornado/blob/master/docs/releases.rst) - [Commits](tornadoweb/tornado@v6.3.1...v6.3.3) --- updated-dependencies: - dependency-name: tornado dependency-type: indirect ... Signed-off-by: dependabot[bot] <support@github.com> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
* Fix unsafe loading from file buffer The numpy documentation states for numpy.frombuffer` that: > This function creates a view into the original object. > This should be safe in general, but it may make sense to copy > the result when the original object is mutable or untrusted. When the filebuffer is mutable a `ValueError: output array is read-only` is raised in: https://github.com/eyurtsev/fcsparser/blob/701000af178e36e0dedb53d409119c25675b9d16/fcsparser/api.py#L590 * Update pyproject.toml --------- Co-authored-by: Eugene Yurtsev <eyurtsev@gmail.com>
* fixed some linting * address a warning raised during tests * update deps * bump fcs_parser version * allow also pandas 1.* * poetry upgrade * Update pyproject.toml --------- Co-authored-by: Eugene Yurtsev <eyurtsev@gmail.com>
* Update lock file * Update
Bumps [urllib3](https://github.com/urllib3/urllib3) from 2.0.6 to 2.0.7. - [Release notes](https://github.com/urllib3/urllib3/releases) - [Changelog](https://github.com/urllib3/urllib3/blob/main/CHANGES.rst) - [Commits](urllib3/urllib3@2.0.6...2.0.7) --- updated-dependencies: - dependency-name: urllib3 dependency-type: indirect ... Signed-off-by: dependabot[bot] <support@github.com> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
* Update README.rst * Update README.rst
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