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Introduction
Installation
Quickstart
Command line interface
Repository layout
The showyourwork.yml config file
The Snakefile
The GitHub action
LaTeX stuff
Zenodo integration
Overleaf integration
Logging
Migrating from previous versions
FAQs
Developer API
cli
cli.commands
cli.commands.build
cli.commands.cache
cli.commands.clean
cli.commands.preprocess
cli.commands.setup
cli.commands.tarball
cli.commands.zenodo
cli.main
exceptions
exceptions.base
exceptions.github
exceptions.latex
exceptions.other
exceptions.overleaf
exceptions.zenodo
config
git
gitapi
logging
overleaf
patches
paths
subproc
tex
userrules
zenodo
arxiv
conda
download
extract
pdf
preprocess
render_dag
arxiv.smk
figure.smk
render_dag.smk
zenodo.smk
compile.smk
conda.smk
dag.smk
preprocess.smk
build.smk
prep.smk
Integration tests
Changelog
Attribution
Projects that use showyourwork
repository
open issue
Index
A
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B
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C
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D
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E
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F
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G
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I
|
J
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L
|
M
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N
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O
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P
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R
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S
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T
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U
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V
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W
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Z
A
arxiv
module
as_dict() (in module showyourwork.config)
B
build() (in module showyourwork.cli.commands.build)
C
cache_restore() (in module showyourwork.cli.commands.cache)
cache_update() (in module showyourwork.cli.commands.cache)
callback() (in module showyourwork.git)
CalledProcessError
check_figure_format() (in module preprocess)
check_for_rate_limit() (in module showyourwork.overleaf)
check_if_user_is_owner() (showyourwork.zenodo.Zenodo method)
clean() (in module showyourwork.cli.commands.clean)
clear_cache() (in module showyourwork.gitapi)
clone() (in module showyourwork.overleaf)
compile_tex() (in module showyourwork.tex)
conda
module
CondaNotFoundError
CondaVersionError
ConfigError
copy_draft() (showyourwork.zenodo.Zenodo method)
create_repo() (in module showyourwork.gitapi)
custom_excepthook() (in module showyourwork.exceptions.base)
D
delete() (showyourwork.zenodo.Zenodo method)
delete_repo() (in module showyourwork.gitapi)
disable_trace() (in module showyourwork.exceptions.base)
download
module
download_file() (showyourwork.zenodo.Zenodo method)
download_file_from_draft() (showyourwork.zenodo.Zenodo method)
download_file_from_record() (showyourwork.zenodo.Zenodo method)
E
echo() (in module showyourwork.cli.main)
edit_yaml() (in module showyourwork.config)
ensure_top_level() (in module showyourwork.cli.main)
entry_point() (in module showyourwork.cli)
extract
module
F
FigureFormatError
FigureGenerationError
FileNotFoundOnZenodo
flatten_dataset_contents() (in module preprocess)
flatten_dict() (in module showyourwork.gitapi)
format() (showyourwork.patches.SnakemakeFormatter method)
G
get_access_token() (in module showyourwork.gitapi)
get_authenticated_user() (in module showyourwork.gitapi)
get_commit_message() (in module showyourwork.git)
get_dataset_dois() (in module showyourwork.zenodo)
get_dataset_urls() (in module showyourwork.zenodo)
get_id_type() (showyourwork.zenodo.Zenodo method)
get_json_tree() (in module preprocess)
get_logger() (in module showyourwork.logging)
get_modified_files() (in module showyourwork.cli.commands.cache)
get_overleaf_credentials() (in module showyourwork.overleaf)
get_repo_branch() (in module showyourwork.git)
get_repo_root() (in module showyourwork.git)
get_repo_sha() (in module showyourwork.git)
get_repo_slug() (in module showyourwork.git)
get_repo_tag() (in module showyourwork.git)
get_repo_url() (in module showyourwork.git)
get_run_type() (in module showyourwork.config)
get_skippable_jobs() (in module showyourwork.patches)
get_snakemake_variable() (in module showyourwork.patches)
get_stdout() (in module showyourwork.subproc)
get_upstream_dependencies() (in module showyourwork.config)
get_workflow_run_status() (in module showyourwork.gitapi)
get_xml_tree() (in module preprocess)
GitHubException
GraphicsPathError
I
InvalidZenodoDOI
InvalidZenodoIdType
InvalidZenodoNotesField
J
job_is_cached() (in module showyourwork.patches)
L
LaTeXException
M
MissingCondaEnvironmentInUserRule
MissingConfigFile
MissingDependencyError
MissingFigureOutputError
MissingGitHubAPIKey
MissingOverleafCredentials
MissingXMLFile
MissingZenodoAccessToken
module
arxiv
conda
download
extract
pdf
preprocess
showyourwork
showyourwork.cli
showyourwork.cli.commands
showyourwork.cli.commands.build
showyourwork.cli.commands.cache
showyourwork.cli.commands.clean
showyourwork.cli.commands.preprocess
showyourwork.cli.commands.setup
showyourwork.cli.commands.tarball
showyourwork.cli.commands.zenodo
showyourwork.cli.main
showyourwork.config
showyourwork.exceptions
showyourwork.exceptions.base
showyourwork.exceptions.github
showyourwork.exceptions.latex
showyourwork.exceptions.other
showyourwork.exceptions.overleaf
showyourwork.exceptions.zenodo
showyourwork.git
showyourwork.gitapi
showyourwork.logging
showyourwork.overleaf
showyourwork.patches
showyourwork.paths
showyourwork.subproc
showyourwork.tex
showyourwork.userrules
showyourwork.zenodo
MultipleOverleafIds
N
NotImplementedError
O
OverleafAuthenticationError
OverleafError
OverleafException
OverleafRateLimitExceeded
P
parse_config() (in module showyourwork.config)
parse_datasets() (in module preprocess)
parse_overleaf() (in module showyourwork.config)
parse_request() (in module showyourwork.subproc)
patch_snakemake_cache() (in module showyourwork.patches)
patch_snakemake_cache_optimization() (in module showyourwork.patches)
patch_snakemake_logging() (in module showyourwork.patches)
patch_snakemake_missing_input_leniency() (in module showyourwork.patches)
patch_snakemake_wait_for_files() (in module showyourwork.patches)
pdf
module
preprocess
module
preprocess() (in module showyourwork.cli.commands.preprocess)
process_run_result() (in module showyourwork.subproc)
process_user_rules() (in module showyourwork.userrules)
publish() (showyourwork.zenodo.Zenodo method)
pull_files() (in module showyourwork.overleaf)
push_files() (in module showyourwork.overleaf)
R
redirect_exception() (in module showyourwork.exceptions.base)
render_config() (in module showyourwork.config)
replacements (showyourwork.patches.SnakemakeFormatter attribute)
RequestError
require_access_token() (in module showyourwork.zenodo)
restore_trace() (in module showyourwork.exceptions.base)
RunDirectiveNotAllowedInUserRules
S
setup() (in module showyourwork.cli.commands.setup)
setup_remote() (in module showyourwork.overleaf)
showyourwork
module
showyourwork (class in showyourwork.paths)
showyourwork.cli
module
showyourwork.cli.commands
module
showyourwork.cli.commands.build
module
showyourwork.cli.commands.cache
module
showyourwork.cli.commands.clean
module
showyourwork.cli.commands.preprocess
module
showyourwork.cli.commands.setup
module
showyourwork.cli.commands.tarball
module
showyourwork.cli.commands.zenodo
module
showyourwork.cli.main
module
showyourwork.config
module
showyourwork.exceptions
module
showyourwork.exceptions.base
module
showyourwork.exceptions.github
module
showyourwork.exceptions.latex
module
showyourwork.exceptions.other
module
showyourwork.exceptions.overleaf
module
showyourwork.exceptions.zenodo
module
showyourwork.git
module
showyourwork.gitapi
module
showyourwork.logging
module
showyourwork.overleaf
module
showyourwork.patches
module
showyourwork.paths
module
showyourwork.subproc
module
showyourwork.tex
module
showyourwork.userrules
module
showyourwork.zenodo
module
ShowyourworkException
ShowyourworkNotFoundError
SnakemakeFormatter (class in showyourwork.patches)
T
tarball() (in module showyourwork.cli.commands.tarball)
TarballExtractionError
TectonicError
U
UnableToInferClassName
upload_file() (showyourwork.zenodo.Zenodo method)
upload_file_to_draft() (showyourwork.zenodo.Zenodo method)
user (class in showyourwork.paths)
V
validate_slug() (in module showyourwork.cli.main)
W
wipe_remote() (in module showyourwork.overleaf)
Z
Zenodo (class in showyourwork.zenodo)
zenodo_create() (in module showyourwork.cli.commands.zenodo)
zenodo_delete() (in module showyourwork.cli.commands.zenodo)
zenodo_freeze() (in module showyourwork.cli.commands.zenodo)
zenodo_publish() (in module showyourwork.cli.commands.zenodo)
ZenodoContentsError
ZenodoDownloadError
ZenodoError
ZenodoException
ZenodoRecordNotFound
ZenodoUploadError