Summarize LSF job properties by parsing log files.

Related tags

Logging lsf_stats
Overview

lsf_stats

PyPI Tests

Summarize LSF job properties by parsing log files of workflows executed by Snakemake.

Installation

$ pip install lsf_stats

Usage

$ lsf_stats --help
Usage: lsf_stats [OPTIONS] COMMAND [ARGS]...

  Summarize LSF job properties by parsing log files.

Options:
  --version  Show the version and exit.
  --help     Show this message and exit.

Commands:
  gather     Aggregate information from log files in single dataframe.
  summarize  Summarize and visualize aggregated information.

Example

Assume that you executed your Snakemake workflow using the lsf-profile and all generated log files are stored in the directory ./logs/:

$ snakemake --profile lsf
[..]

You can then quickly aggregate resource, rule and other types of information about the workflow execution into a single dataframe:

$ lsf_stats gather -o workflow_stats.csv.gz ./logs/
[..]

This dataframe can then be summarized in various ways:

$ lsf_stats summarize \
    --query 'status == "Successfully completed."' \
    --split-wildcards \
    --grouping-variable category \
    workflow_stats.csv.gz
[..]

For example, the following plots will be generated:

Job execution Job resources
Job execution Job resources
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Comments
  • Update seaborn requirement from ^0.11.1 to >=0.11.1,<0.13.0

    Update seaborn requirement from ^0.11.1 to >=0.11.1,<0.13.0

    Updates the requirements on seaborn to permit the latest version.

    Release notes

    Sourced from seaborn's releases.

    v0.12.0

    Introduction of the objects interface

    This release debuts the seaborn.objects interface, an entirely new approach to making plots with seaborn. It is the product of several years of design and 16 months of implementation work. The interface aims to provide a more declarative, composable, and extensible API for making statistical graphics. It is inspired by Wilkinson's grammar of graphics, offering a Pythonic API that is informed by the design of libraries such as ggplot2 and vega-lite along with lessons from the past 10 years of seaborn's development.

    For more information and numerous examples, see the tutorial chapter and API reference.

    This initial release should be considered "experimental". While it is stable enough for serious use, there are definitely some rough edges, and some key features remain to be implemented. It is possible that breaking changes may occur over the next few minor releases. Please be patient with any limitations that you encounter and help the development by reporting issues when you find behavior surprising.

    Keyword-only arguments

    Seaborn's plotting functions now require explicit keywords for most arguments, following the deprecation of positional arguments in v0.11.0. With this enforcement, most functions have also had their parameter lists rearranged so that data is the first and only positional argument. This adds consistency across the various functions in the library. It also means that calling func(data) will do something for nearly all functions (those that support wide-form data) and that pandas.DataFrame can be piped directly into a plot. It is possible that the signatures will be loosened a bit in future releases so that x and y can be positional, but minimal support for positional arguments after this change will reduce the chance of inadvertent mis-specification (2804).

    Modernization of categorical scatterplots

    This release begins the process of modernizing the categorical plots, beginning with stripplot and swarmplot. These functions are sporting some enhancements that alleviate a few long-running frustrations (2413, 2447):

    • The new native_scale parameter allows numeric or datetime categories to be plotted with their original scale rather than converted to strings and plotted at fixed intervals.
    • The new formatter parameter allows more control over the string representation of values on the categorical axis. There should also be improved defaults for some types, such as dates.
    • It is now possible to assign hue when using only one coordinate variable (i.e. only x or y).
    • It is now possible to disable the legend.

    The updates also harmonize behavior with functions that have been more recently introduced. This should be relatively non-disruptive, although a few defaults will change:

    • The functions now hook into matplotlib's unit system for plotting categorical data. (Seaborn's categorical functions actually predate support for categorical data in matplotlib.) This should mostly be transparent to the user, but it may resolve a few edge cases. For example, matplotlib interactivity should work better (e.g., for showing the data value under the cursor).
    • A color palette is no longer applied to levels of the categorical variable by default. It is now necessary to explicitly assign hue to see multiple colors (i.e., assign the same variable to x/y and hue). Passing palette without hue will continue to be honored for one release cycle.
    • Numeric hue variables now receive a continuous mapping by default, using the same rules as scatterplot. Pass palette="deep" to reproduce previous defaults.
    • The plots now follow the default property cycle; i.e. calling an axes-level function multiple times with the same active axes will produce different-colored artists.
    • Currently, assigning hue and then passing a color will produce a gradient palette. This is now deprecated, as it is easy to request a gradient with, e.g. palette="light:blue".

    Similar enhancements / updates should be expected to roll out to other categorical plotting functions in future releases. There are also several function-specific enhancements:

    • In stripplot, a "strip" with a single observation will be plotted without jitter (2413)
    • In swarmplot, the points are now swarmed at draw time, meaning that the plot will adapt to further changes in axis scaling or tweaks to the plot layout (2443).
    • In swarmplot, the proportion of points that must overlap before issuing a warning can now be controlled with the warn_thresh parameter (2447).
    • In swarmplot, the order of the points in each swarm now matches the order in the original dataset; previously they were sorted. This affects only the underlying data stored in the matplotlib artist, not the visual representation (2443).

    More flexible errorbars

    Increased the flexibility of what can be shown by the internally-calculated errorbars for lineplot, barplot, and pointplot.

    With the new errorbar parameter, it is now possible to select bootstrap confidence intervals, percentile / predictive intervals, or intervals formed by scaled standard deviations or standard errors. The parameter also accepts an arbitrary function that maps from a vector to an interval. There is a new user guide chapter demonstrating these options and explaining when you might want to use each one.

    As a consequence of this change, the ci parameter has been deprecated. Note that regplot retains the previous API, but it will likely be updated in a future release (2407, 2866).

    Other updates

    • It is now possible to aggregate / sort a lineplot along the y axis using orient="y" (2854).
    • Made it easier to customize FacetGrid / PairGrid / JointGrid with a fluent (method-chained) style by adding apply/ pipe methods. Additionally, fixed the tight_layout and refline methods so that they return self (2926).
    • Added FacetGrid.tick_params and PairGrid.tick_params to customize the appearance of the ticks, tick labels, and gridlines of all subplots at once (2944).

    ... (truncated)

    Commits
    • 231f1ba Merge branch 'master' into v0.12
    • 6a17b60 Move position in FAQ page
    • 9ebc3c5 Merge branch 'master' into v0.12
    • 57a0b54 Add v0.11 docs to archive dropdown
    • cce7b5d Update version for v0.12.0 release
    • cb9012c Merge branch 'master' into v0.12
    • 0dfd322 Documentation tweaks upon pre-release review
    • cd27698 Remove setup.py file
    • 73cb84f Merge branch 'master' into v0.12
    • e150cec Fix tutorial crossref
    • Additional commits viewable in compare view

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  • Update humanize requirement from ^3.9.0 to >=3.9,<5.0

    Update humanize requirement from ^3.9.0 to >=3.9,<5.0

    Updates the requirements on humanize to permit the latest version.

    Release notes

    Sourced from humanize's releases.

    4.0.0

    Removed

    Commits
    • a1514eb Merge pull request #239 from hugovk/rm-3.6
    • 48506d4 pre-commit autoupdate
    • 8f2c855 Remove unused import
    • 04bf887 Drop support for Python 3.6
    • 0f2ff42 Use actions/setup-python's pip cache and update other CI config
    • 464de59 Merge pull request #253 from hugovk/rm-VERSION
    • 66b8a63 Merge pull request #250 from carterbox/no-overflow-naturaldelta
    • e89c8c8 Merge pull request #241 from samueljsb/remove-deprecated-private-function-ali...
    • ffe4bcf Remove deprecated VERSION, use version instead
    • eb3e253 Merge branch 'master' into no-overflow-naturaldelta
    • Additional commits viewable in compare view

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    dependencies 
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  • Update black requirement from ^21.6b0 to ^22.1

    Update black requirement from ^21.6b0 to ^22.1

    Updates the requirements on black to permit the latest version.

    Release notes

    Sourced from black's releases.

    22.1.0

    At long last, Black is no longer a beta product! This is the first non-beta release and the first release covered by our new stability policy.

    Highlights

    • Remove Python 2 support (#2740)
    • Introduce the --preview flag (#2752)

    Style

    • Deprecate --experimental-string-processing and move the functionality under --preview (#2789)
    • For stubs, one blank line between class attributes and methods is now kept if there's at least one pre-existing blank line (#2736)
    • Black now normalizes string prefix order (#2297)
    • Remove spaces around power operators if both operands are simple (#2726)
    • Work around bug that causes unstable formatting in some cases in the presence of the magic trailing comma (#2807)
    • Use parentheses for attribute access on decimal float and int literals (#2799)
    • Don't add whitespace for attribute access on hexadecimal, binary, octal, and complex literals (#2799)
    • Treat blank lines in stubs the same inside top-level if statements (#2820)
    • Fix unstable formatting with semicolons and arithmetic expressions (#2817)
    • Fix unstable formatting around magic trailing comma (#2572)

    Parser

    • Fix mapping cases that contain as-expressions, like case {"key": 1 | 2 as password} (#2686)
    • Fix cases that contain multiple top-level as-expressions, like case 1 as a, 2 as b (#2716)
    • Fix call patterns that contain as-expressions with keyword arguments, like case Foo(bar=baz as quux) (#2749)
    • Tuple unpacking on return and yield constructs now implies 3.8+ (#2700)
    • Unparenthesized tuples on annotated assignments (e.g values: Tuple[int, ...] = 1, 2, 3) now implies 3.8+ (#2708)
    • Fix handling of standalone match() or case() when there is a trailing newline or a comment inside of the parentheses. (#2760)
    • from __future__ import annotations statement now implies Python 3.7+ (#2690)

    Performance

    • Speed-up the new backtracking parser about 4X in general (enabled when --target-version is set to 3.10 and higher). (#2728)
    • Black is now compiled with mypyc for an overall 2x speed-up. 64-bit Windows, MacOS, and Linux (not including musl) are supported. (#1009, #2431)

    Configuration

    • Do not accept bare carriage return line endings in pyproject.toml (#2408)
    • Add configuration option (python-cell-magics) to format cells with custom magics in Jupyter Notebooks (#2744)
    • Allow setting custom cache directory on all platforms with environment variable BLACK_CACHE_DIR (#2739).
    • Enable Python 3.10+ by default, without any extra need to specify --target-version=py310. (#2758)
    • Make passing SRC or --code mandatory and mutually exclusive (#2804)

    Output

    • Improve error message for invalid regular expression (#2678)
    • Improve error message when parsing fails during AST safety check by embedding the underlying SyntaxError (#2693)
    • No longer color diff headers white as it's unreadable in light themed terminals (#2691)
    • Text coloring added in the final statistics (#2712)
    • Verbose mode also now describes how a project root was discovered and which paths will be formatted. (#2526)

    Packaging

    • All upper version bounds on dependencies have been removed (#2718)
    • typing-extensions is no longer a required dependency in Python 3.10+ (#2772)
    • Set click lower bound to 8.0.0 as Black crashes on 7.1.2 (#2791)

    ... (truncated)

    Changelog

    Sourced from black's changelog.

    22.1.0

    At long last, Black is no longer a beta product! This is the first non-beta release and the first release covered by our new stability policy.

    Highlights

    • Remove Python 2 support (#2740)
    • Introduce the --preview flag (#2752)

    Style

    • Deprecate --experimental-string-processing and move the functionality under --preview (#2789)
    • For stubs, one blank line between class attributes and methods is now kept if there's at least one pre-existing blank line (#2736)
    • Black now normalizes string prefix order (#2297)
    • Remove spaces around power operators if both operands are simple (#2726)
    • Work around bug that causes unstable formatting in some cases in the presence of the magic trailing comma (#2807)
    • Use parentheses for attribute access on decimal float and int literals (#2799)
    • Don't add whitespace for attribute access on hexadecimal, binary, octal, and complex literals (#2799)
    • Treat blank lines in stubs the same inside top-level if statements (#2820)
    • Fix unstable formatting with semicolons and arithmetic expressions (#2817)
    • Fix unstable formatting around magic trailing comma (#2572)

    Parser

    • Fix mapping cases that contain as-expressions, like case {"key": 1 | 2 as password} (#2686)
    • Fix cases that contain multiple top-level as-expressions, like case 1 as a, 2 as b (#2716)
    • Fix call patterns that contain as-expressions with keyword arguments, like case Foo(bar=baz as quux) (#2749)
    • Tuple unpacking on return and yield constructs now implies 3.8+ (#2700)
    • Unparenthesized tuples on annotated assignments (e.g values: Tuple[int, ...] = 1, 2, 3) now implies 3.8+ (#2708)
    • Fix handling of standalone match() or case() when there is a trailing newline or a comment inside of the parentheses. (#2760)
    • from __future__ import annotations statement now implies Python 3.7+ (#2690)

    Performance

    • Speed-up the new backtracking parser about 4X in general (enabled when --target-version is set to 3.10 and higher). (#2728)
    • Black is now compiled with mypyc for an overall 2x speed-up. 64-bit Windows, MacOS, and Linux (not including musl) are supported. (#1009, #2431)

    ... (truncated)

    Commits

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  • Update black requirement from ^20.8b1 to ^21.6b0

    Update black requirement from ^20.8b1 to ^21.6b0

    Updates the requirements on black to permit the latest version.

    Release notes

    Sourced from black's releases.

    21.6b0

    Black

    • Fix failure caused by fmt: skip and indentation (#2281)
    • Account for += assignment when deciding whether to split string (#2312)
    • Correct max string length calculation when there are string operators (#2292)
    • Fixed option usage when using the --code flag (#2259)
    • Do not call uvloop.install() when Black is used as a library (#2303)
    • Added --required-version option to require a specific version to be running (#2300)
    • Fix incorrect custom breakpoint indices when string group contains fake f-strings (#2311)
    • Fix regression where R prefixes would be lowercased for docstrings (#2285)
    • Fix handling of named escapes (\N{...}) when --experimental-string-processing is used (#2319)
    Changelog

    Sourced from black's changelog.

    21.6b0

    Black

    • Fix failure caused by fmt: skip and indentation (#2281)
    • Account for += assignment when deciding whether to split string (#2312)
    • Correct max string length calculation when there are string operators (#2292)
    • Fixed option usage when using the --code flag (#2259)
    • Do not call uvloop.install() when Black is used as a library (#2303)
    • Added --required-version option to require a specific version to be running (#2300)
    • Fix incorrect custom breakpoint indices when string group contains fake f-strings (#2311)
    • Fix regression where R prefixes would be lowercased for docstrings (#2285)
    • Fix handling of named escapes (\N{...}) when --experimental-string-processing is used (#2319)

    Integrations

    • The vim plugin now searches upwards from the directory containing the current buffer instead of the current working directory for pyproject.toml. (#1871)

    Integrations

    • The vim plugin now reads the correct string normalization option in pyproject.toml (#1869)
    • The vim plugin no longer crashes Black when there's boolean values in pyproject.toml (#1869)

    21.5b2

    Black

    • A space is no longer inserted into empty docstrings (#2249)
    • Fix handling of .gitignore files containing non-ASCII characters on Windows (#2229)
    • Respect .gitignore files in all levels, not only root/.gitignore file (apply .gitignore rules like git does) (#2225)
    • Restored compatibility with Click 8.0 on Python 3.6 when LANG=C used (#2227)
    • Add extra uvloop install + import support if in python env (#2258)
    • Fix --experimental-string-processing crash when matching parens are not found (#2283)
    • Make sure to split lines that start with a string operator (#2286)
    • Fix regular expression that black uses to identify f-expressions (#2287)

    Blackd

    • Add a lower bound for the aiohttp-cors dependency. Only 0.4.0 or higher is supported. (#2231)

    Integrations

    • The official Black action now supports choosing what version to use, and supports the

    ... (truncated)

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    dependencies 
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Log processor for nginx or apache that extracts user and user sessions and calculates other types of useful data for bot detection or traffic analysis

Log processor for nginx or apache that extracts user and user sessions and calculates other types of useful data for bot detection or traffic analysis

David Puerta Martín 1 Nov 11, 2021