v0.8.5

2024/6/19 21:29:28

Focus on

1. Fix bugs in bio.Peptide function assembly
2. Fix code in web.utils.TaskPool function assembly

What's New

• addon: add mbapy\bio\high_level.py as sub-module

Minor Addon

• minor addon: mbapy\bio\high_level.py: add calcu_peptide_mutations
• minor addon: mbapy\sci_instrument\mass_base.py: MassData: add add_match_record
• minor addon: mbapy\file.py: write_sheets: add writer_kwgs and kwargs
• minor addon: mbapy\sci_instrument\mass_base.py: MassData: ESI_IRON_MODE: add [M+2H]2+ and [M+3H]3+
• minor addon: mbapy\sci_instrument\mass_base.py: MassData: add_match_record: add charge
• minor addon: mbapy\scripts\mass.py: plot-mass: add legend_bbox arg
• minor-addon: mbapy\sci_instrument\mass_utils.py:plot_mass: support plot match_df tag
• minor addon: mbapy\sci_instrument\hplc_base.py: HplcData: add method: calcu_single_peak_area
• minor addon: mbapy\scripts\hplc.py: explore-hplc: add manual peak area integrate

BUG-FIX

• fix-bug: mbapy\sci_instrument_base.py: SciInstrumentData: save_processed_data: do not save index now
• fix-bug: mbapy\sci_instrument\hplc\waters.py: WatersData: save_processed_data: do not save index now
• fix-bug: mbapy\sci_instrument\mass_base.py: MassData: save_processed_data: do not save index now
• fix-bug: mbapy\sci_instrument\hplc\waters.py: WatersData: get_abs_data: return refined_abs_data if need

CODE-FIX

• fix-code: mbapy\sci_instrument\mass_base.py: MassData: add match_df
• fix-code: mbapy\sci_instrument\mass\SCIEX.py: SciexPeakListData: process_raw_data: Monoisotopic as bool
• fix-code: mbapy\scripts\peptide.py: fit_mass: use match_df
• fix-code: mbapy\scripts\peptide.py: fit_mass: only fit Monoisotopic now
• fix-code: mbapy\scripts\peptide.py: fit_mass: minor changes
• fix-code: mbapy\sci_instrument\hplc_utils.py: plot_hplc: use refined_abs_data to get abs data
• fix-code: mbapy\sci_instrument\hplc_utils.py: plot_hplc: minus refine number now
• fix-code: mbapy\scripts\hplc.py: explore-hplc: _ui_refinment_numbers use tag2label now

Remove

None or a little.

Other Changes

• fix-code: requirements.json: matplotlib requires version >=3.7.5

Details

完整的更新日志: https://gitee.com/bhm-bob/BA_PY/commits/v0.8.5
Full Changelog: v0.8.4...v0.8.5

v0.8.4

2024-06-16 10:54:32

Focus on

1. Fix bugs in bio.Peptide function assembly
2. Fix code in web.utils.TaskPool function assembly

What's New

None or a little.

Minor Addon

• minor add: mbapy\web_utils\task.py: TaskPool: add method: query_single_task_from_tasks
• minor addon: mbapy\bio\peptide.py: add eq for AnimoAcid and Peptide

BUG-FIX

• fix-bug: mbapy\sci_instrument\mass_utils.py & mbapy\scripts\mass.py: handle is_y_log rightly
• fix-bug: mbapy\scripts\peptide.py: fit_mass: make_args: add missing argument 'mass'
• fix-bug: mbapy\scripts\peptide.py: fit_mass: process_args: only extend unique seq now

CODE-FIX

• fix-code: mbapy\scripts\mass.py: plot_mass: load_suffix_data: using task_pool.query_single_task_from_tasks instead of task_pool.query_task
• fix-code: mbapy\scripts\mass.py: explore_mass: main_process: using Thread to load data in background
• fix-code: mbapy\sci_instrument_utils.py: add all

Remove

None or a little.

Other Changes

None or a little.

Details

完整的更新日志: https://gitee.com/bhm-bob/BA_PY/commits/v0.8.4

v0.8.3

2024/6/13 10:30:34

Focus on

1. Fix bugs in Mass function assembly
2. Add new command: fit-mass

What's New

• addon: mbapy\scripts_script_utils_.py: add _print
• addon: mbapy\scripts\peptide.py: add new command: fit-mass

Minnor Addon

• minnor-addon: mbapy\sci_instrument\mass_base.py: MassData: add ESI_IRON_MODE attr fix-bug: mbapy\sci_instrument\mass_base.py: MassData.search_peaks: consider egde when concatenate y_list_r

BUG-FIX

• fix-bug: mbapy\web_utils\task.py: TaskPool: query_task: now block when block param is true and task is not returned by the query and is not timeout
• fix-bug: mbapy\scripts\mass.py: plot-mass: set CHARGE_HEADER depend on mass and X_M_HEADER
• fix-bug: mbapy\sci_instrument\hplc_utils.py: recover x, y offset is right now
• fix-bug: mbapy\scripts\hplc.py: args.file_labels now add default labels when no file labels given

CODE-FIX

• fix-code: mbapy\sci_instrument\mass_utils.py & mbapy\scripts\mass.py: support is_y_log option
• fix-code: mbapy\file.py: opts_file: add gzip option for pkl
• fix-code: mbapy\scripts\peptide.py: re-construct the function calcu_mw_of_mutations to Command class

Remove

None or a little.

Other Changes

Storage

• fix-code: requirements.json: add tqdm into 'std'

Details

完整的更新日志: https://gitee.com/bhm-bob/BA_PY/commits/v0.8.3

v0.8.2

2024-06-10 21:58:55

Focus on

1. Fix bugs in HPLC and Mass function assembly

What's New

None or a little.

BUG-FIX

• fix-bug: mbapy\web_utils\task.py: TaskPool: query_task: now block when block param is true and task is not returned by the query and is not timeout
• fix-bug: mbapy\scripts\mass.py: plot-mass: set CHARGE_HEADER depend on mass and X_M_HEADER
• fix-bug: mbapy\sci_instrument\hplc_utils.py: recover x, y offset is right now
• fix-bug: mbapy\scripts\hplc.py: args.file_labels now add default labels when no file labels given

CODE-FIX

• fix-code: mbapy\scripts_main_.py: forword scripts exec name to scripts name
• mbapy\scripts: rename some scripts' name
• fix-code: mbapy\sci_instrument\mass_base.py: MassData: add CHARGE_HEADER attr
• fix-code: mbapy\sci_instrument\mass\SCIEX.py: SciexPeakListData: add attr: CHARGE_HEADER
• fix-code: mbapy\sci_instrument\mass_utils.py: plot_mass: support plot charge text
• fix-code: mbapy\scripts\hplc.py: plot-hplc: support multi-process plotting
• fix-code: mbapy\sci_instrument\hplc_utils.py: plot_hplc: change default fig size
• fix-code: mbapy\sci_instrument\mass_utils.py: add dev-code
• fix-code: mbapy\scripts\mass.py: fix import

Remove

None or a little.

Other Changes

Storage

• fix-code: mbapy\storage\mbapy-cli-scripts-list.json: add copy_file for cp as a new exec_name

Details

完整的更新日志: https://gitee.com/bhm-bob/BA_PY/commits/v0.8.2
Full Changelog: v0.8.1...v0.8.2

v0.8.1

2024/6/6 10:49:03

Focus on

1. Fix GUI version scripts for scripts/mass::plot-mass and scripts/hplc::plot-hplc
2. add area calculation function for sci_instruments.hplc._base and plot ability for sci_instruments.hplc._utils

What's New

• addon: mbapy\sci_instrument\hplc_base.py: HplcData: add search_peaks, calcu_peaks_area, get_area

BUG-FIX

• fix-bug: mbapy\sci_instrument\hplc_utils.py: plot_hplc: check peaks_idx before get from areas_info
• fix-bug: mbapy\sci_instrument\hplc_utils.py: search_peaks use minute now

CODE-FIX

• fix-code: mbapy\sci_instrument\hplc_utils.py: plot_hplc: support plot peak-line, underline, area
• fix-code: mbapy\scripts\hplc.py: explore-hplc: support plot peak-line, underline, area
• fix-code: mbapy\scripts\hplc.py: explore-hplc: add area_percent_df_panel

Remove

None or a little.

Other Changes

Storage

• fix-code: MANIFEST.in: add mbapy/storage/icons/scripts-hplc-peak.png

Details

完整的更新日志: https://gitee.com/bhm-bob/BA_PY/commits/v0.8.1
Full Changelog: v0.8.0...v0.8.1

v0.8.0

Focus on

1. Fix GUI version scripts for scripts/mass::plot-mass and scripts/hplc::plot-hplc
2. add sci_instrument sub-module to obtain HPLC and Mass function assemble in scripts/mass::plot-mass and scripts/hplc::plot-hplc

What's New

• addon: add sci_instruments.hplc as sub-module
• addon: add sci_instruments.hplc._base as sub-module
• addon: add sci_instruments.hplc._utils as sub-module
• addon: add sci_instruments.hplc.waters as sub-module
• addon: add sci_instrument.hplc.SCIEX as sub-module and it's test file
• addon: add sci_instrument._base as sub-module
• addon: add mbapy.sci_instrument.mass as sub-module
• addon: add mbapy.sci_instrument.mass.SCIEX as sub-module
• addon: add sci_instrument._utils as sub-module
• addon: add sci_instrument.mass._utils.plot_mass
• addon: mbapy\sci_instrument_utils.py: add process_num_label_col_marker

BUG-FIX

• fix-bug: scripts/mass: plot-mass: mass option will make right effect on the plot
• fix-bug: sci_instrument.hplc._utils.plot_hplc: dfs_refinment_x now make effect on start_search_time in each fix-code: sci_instrument.hplc: add TICKS_IN_MINUTE
• fix-bug: scripts/hplc: explore_hplc.load_data now load data into stored_dfs
• fix-bug: web.task.TaskPool.wait_till: now will _query_task_queue each time in a loop
• fix-bug: mbapy\sci_instrument_base.py: SciInstrumentData.check_processed_data_empty: use processed_data param now
• fix-bug: mbapy\sci_instrument\mass_base.py: MassData.load_processed_data_file: check headers now

CODE-FIX

• fix-code: scripts/hplc: explore-hplc: add peak_legend_loc option
• fix-code: scripts/hplc: explore-hplc: set min_height's default value from 0 to 0.01
• fix-code: plot.save_show: add kwargs
• fix-code: scripts/hplc: explore-hplc: add end_search_time and line_width option
• fix-code: scripts/hplc: explore-hplc: use bbox_extra_artists to include legend while saving
• fix-code: scripts/hplc: explore-hplc: add refinment option
• fix-code: scripts/hplc: explore-hplc: add url and port arg
• fix-code: scripts/hplc: explore-hplc: add bind lim option
• fix-code: scripts/mass: explore-hplc: add y-lim option
• fix-code: scripts/hplc: explore-hplc: add refinment option for y-data
• fix-code: scripts/mass: explore-mass: GUI minor fix
• fix-code: scripts/hplc: use sci_instrument.hplc sub-module now
• fix-code: scripts/hplc: use sci_instrument.hplc now
• fix-code: add web.task.TaskPool.wait_till_tasks_done
• fix-code: sci_instrument._base.SciInstrumentData.check_processed_data_empty: add processed_data param
• fix-code: sci_instrument.hplc._utils: move process_file_labels and process_peak_labels to sci_instrument._utils
• fix-code: sci_instrument.mass._base.MassData.search_peaks: add parallel option
• fix-code: sci_instrument.mass.SCIEX.SciexPeakListData: process_raw_data now make self.peak_df as self.data_df.copy()
• fix-code: mbapy.sci_instrument.mass.SCIEX: support load xlsx
• fix-code: mbapy\sci_instrument_base.py: SciInstrumentData: add DATA_FILE_SUFFIX and RECOMENDED_DATA_FILE_SUFFIX attr
• fix-code: mbapy\sci_instrument\mass_base.py: MassData: add X_MZ_HEADER and X_M_HEADER attr
• fix-code: mbapy\sci_instrument\mass_utils.py: plot_mass: works now
• fix-code: mbapy\sci_instrument\mass\SCIEX.py: SciexPeakListData and SciexPeakListData: add X_MZ_HEADER and X_M_HEADER attr
• fix-code: mbapy\scripts\mass.py: use mbapy\sci_instrument\mass sub-module now
• fix-code: mbapy\plot.py: add PLT_MARKERS
• fix-code: mbapy\sci_instrument\mass_utils.py: plot_mass: add marker
• fix-code: mbapy\scripts\mass.py: add marker

Remove

None or a little.

Other Changes

Storage

• addon: add icon: storage/icons/scripts-hplc-peak.png

Details

完整的更新日志: https://gitee.com/bhm-bob/BA_PY/commits/v0.8.0

v0.7.4

Focus on

1. Add GUI version scripts for scripts/mass::plot-mass and scripts/hplc::plot-hplc
2. web_utils.task.TaskPool

What's New

1. addon: add new sub-module: plot_utils.bar_utils, as bar-stuff in plot sub-module
2. add test/plot_utils/test_bar_utils.py
3. addon: add new sub-module: plot_utils.scatter_utils
4. addon: add thread mode in web_utils.task.TaskPool
5. addon: scripts.scripts_utils: add Command class for making a new way to build a command
6. addon: scripts.scripts_utils: add excute_command func for making a new way to excuting a command
7. addon: scripts/mass: add new command 'explore-mass' to config args with webGUI via nicegui
8. addon: scripts/hplc: add 'explore-hplc': plot HPLC fig with NiceGUI

FIX-BUG

1. fix-bug: web_utils.task.TaskPool.close: now stop _async_loop befor close
2. fix-bug: webutils.task.TaskPool._run_process_loop: remove task after exception
3. fix-bug: web_utils.task.TaskPool get result in a safe way in async mode
4. fix-bug: scripts/peptide: mmw: opts_file works with right params
5. fix-bug: scripts/hplc: explore-hplc: search peaks using prominence instead height
6. fix-bug: scripts/mass: explore-mass: close un-closed fig before plot to avoid multi fig window
7. fix-bug: scripts/mass: explore-mass: now use same name as 'plot-mass' to load peaks cache
8. fix-bug: scripts/mass: explore-mass: now update labels in make_fig to avoid process error on input
9. fix-bug: scripts/mass: explore-mass: fix label color error
10. fix-bug: scripts/mass: plot-mass & explore-mass: recovery output path if use_recursive_output
11. fix-bug: scripts/mass: explore-mass: make right path for saving fig

FIX-CODE

1. fix-code: web_utils.task.TaskPool add process mode
2. fix-code: web_utils.task.TaskPool: add count_waiting_tasks and count_done_tasks
3. fix-code: web_utils.task.TaskPool: add wait_till
4. fix-code: scripts/peptide: mmw: add multi-process and disable-verbose option
5. fix-code: scripts/peptide: mmw: support any multi_processs number
6. fix-code: scripts/peptide: mmw: add --disable-low-memory option
7. fix-code: scripts/peptide: mmw: only apply --disable-verbose option in mutation output
8. fix-code: bio.peptide: Peptide.init: set AAs=[] if repr is None
9. fix-code: bio.peptide: Peptide.flatten: return seq if inplace is True
10. fix-code: scripts/peptide: mmw: mutate each AA instead of entire seq to optimze speed
11. fix-code: web_utils.task: TaskPool.add_task: use uuid4 to generate default name instead of f'time.time():.6f'
12. fix-code: scripts/extract-dir: skip when dist is source, add option to remove empty dir
13. fix-code: plot: save_show: add show param
14. fix-code: plot.get_palette accept other mode

Remove

None or a little.

Other Changes

requirements

1. add ujson to full set
2. add pygame and nicegui to [bio] add nicegui to [full]

Details

完整的更新日志: https://gitee.com/bhm-bob/BA_PY/commits/v0.7.4
Full Changelog: v0.7.3...v0.7.4

v0.7.3

Focus on

1. Add new function in web_utils
2. Reconstruct plot and add new function

What's New

1. addon: add new sub-module: plot_utils.bar_utils, as bar-stuff in plot sub-module
2. add test/plot_utils/test_bar_utils.py
3. addon: add new sub-module: plot_utils.scatter_utils
4. addon: add thread mode in web_utils.task.TaskPool

FIX-BUG

1. fix-bug: web_utils.request.Browser.get return page_source instead of None
2. fix-bug: base.parameter_checker now support check default value

FIX-CODE

1. fix-code: stats.reg: add equation in returns
2. fix-code: scripts/mass.py and hplc.py: set legend draggable
3. fix-code: remove plot import in plot_utils.scatter_utils
4. fix-code: plot_utils.bar_utils.plot_bar: add figsize, dpi, hatchs, ylabel params
5. fix-code: plot_utils.bar_utils.plot_bar: remove fig param
6. fix-code: plot: add all
7. fix-code: rename web_utils.task.CoroutinePool to web_utils.task.TaskPool
8. fix-cdeo: web_utils.spider support web_utils.task.TaskPool

Remove

None or a little.

Other Changes

docs

1. add more docs

Details

完整的更新日志: https://gitee.com/bhm-bob/BA_PY/commits/v0.7.3
Full Changelog: v0.7.2...v0.7.3

v0.7.2

Focus on

1. Fix bug in scripts
2. Fix bug in plot
3. Add new scripts

What's New

1. addon: plot.plot_bar: add xticks_pad param
2. addon: add stats.test.auto_ind_test
3. fix-code: add jitter option to plot.plot_bar
4. fix-code: scripts.script_utils.show_args: add printf param
5. fix-code: scripts/peptide.py: mmw: add --disable-aa-deletion option
6. addon: add new scripts: file-size.py
7. addon: add new scripts/hplc.py
8. fix-code: scripts/hplc.py: plot-hplc: add merge option
9. fix-code: scripts/mass.py: plot-mass: add args to control legend pos

FIX-BUG

1. fix-bug: file.get_paths_with_extension: use os.listdir instead of os.walk to avoid unexpected files update
2. fix-bug: plot.plot_bar: set_xlim set right max-lim

FIX-CODE

1. fix-code: plot.plot_bar set y-axis fontsize as first x-axis
2. fix-code: plot.plot_bar accept non-string sub-factors, convert by str()
3. fix-code: add version req to seaborn because swarmplot
4. fix-code: mass.py: plot-mass: find peaks first, then filter
5. fix-code: examples/plot/dev.py: fix import
6. fix-code: stats.df.pro_bar_data_R fix comment
7. fix-code: add more info when get unkown scripts
8. fix-code: scripts/file-size.py: add sort option
9. fix-code: plot.plot_bar: err_kwargs.ecolor support list as a input
10. fix-code: scripts.main: move scripts_info into storage dir as a json file to allow dynamic changes
11. fix-code: scripts.main.exec_scripts: allow exec scripts with no args
12. fix-code: scripts/hplc.py: plot-hplc: support recursive output
13. minor changes: scripts/mass.py: plot-mass: update dpi to 600
14. fix-code: scripts/mass.py: plot-mass: add peaks cache
15. fix-code: scripts/mass.py: plot-mass: support recursive mode

Remove

None or a little.

Other Changes

requirements.json

1. move PyPDF2 to std

Details

完整的更新日志: https://gitee.com/bhm-bob/BA_PY/commits/v0.7.2
Full Changelog: v0.7.1...v0.7.2

v0.7.1

v0.7.1b1

BUF-FIX

1. fix-bug: plot.get_palette hls for all n number
2. fix-bug: bio.peptide.AnimoAcid: fix Gly mfd
3. fix-bug: bio.peptide.AnimoAcid.get_molecular_formula_dict: C_protect noly minus one H when isn't OH now
4. fix-bug: add MyArgs.get_args which is removed by commit 8a7d344

Detail

1. v0.7.1b1
2. fix-code: file_utils.video.extract_unique_frames: add torch_device param
3. fix-code: file: add all
4. fix-bug: plot.get_palette hls for all n number
5. fix-code: scrits.main.main: add '\n' in the end of the output
6. fix-bug: bio.peptide.AnimoAcid: fix Gly mfd
7. fix-code: scripts/peptide.py: add AA number in mmw output
8. fix-bug: add MyArgs.get_args which is removed by commit 8a7d344
9. addon: add method: web_utils.task.CoroutinePool.check_empty
10. addon: add extract audio imp for scripts/video.py

完整的更新日志: https://gitee.com/bhm-bob/BA_PY/compare/v0.7.0...v0.7.1b1
Full Changelog: v0.7.0...v0.7.1

v0.7.1

Focus on

1. fix BUGs in plot and stats sub-module

What's New

1. addon: plot.plot_bar support setting for first xlabel offset
2. addon: plot.plot_bar support linewidth, log and ecolor params
3. addon: plot.pro_hue_pos support hue_space param
4. addon: add plot.plot_stats_star
5. addon: add stats.reg.quadratic_reg
6. add test/stats/test_reg.py
7. addon: add stats.test.wilcoxon
8. addon: add plot.calcu_swarm_pos

BUG-FIX

1. fix-bug: stats.test._get_x1_x2 return (N, ) shape instead of (N, 1) so on

CODE-FIX

1. fix-code: plot.pro_hue_pos support asymmetric grouping
2. fix-code: plot.plot_bar support hue_space and bar_space
3. fix-code: plot.plot_bar support linewidth
4. fix-code: scripts/mass.py: plot-mass now support Mass/Charge data and absorbance data

Remove

None or a little.

Other Changes

None or a little.

Details

完整的更新日志: https://gitee.com/bhm-bob/BA_PY/commits/v0.7.1
Full Changelog: v0.7.1...v0.7.1