Index A | B | C | D | E | F | G | I | J | K | L | M | N | O | P | R | S | T | U | V | W | Z A args (showyourwork.cli.main.option_spec attribute) 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_setup module CondaNotFoundError CondaVersionError ConfigError convert_to_png() (in module render_dag) copy_and_fix_synctex module copy_draft() (showyourwork.zenodo.Zenodo method) create_repo() (in module showyourwork.gitapi) custom_excepthook() (in module showyourwork.exceptions.base) cwd_as() (in module showyourwork.cli.main) 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) 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 render_dag) (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 is_relative_to() (in module render_dag) J job_is_cached() (in module showyourwork.patches) K kwargs (showyourwork.cli.main.option_spec attribute) L LaTeXException M main_command() (in module showyourwork.cli.main) MissingCondaEnvironmentInUserRule MissingConfigFile MissingDependencyError MissingFigureOutputError MissingGitHubAPIKey MissingOverleafCredentials MissingXMLFile MissingZenodoAccessToken module arxiv compile_setup copy_and_fix_synctex download extract preprocess render_dag 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.run_snakemake 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.userrules showyourwork.zenodo MultipleOverleafIds N NotImplementedError O option_spec (class in showyourwork.cli.main) 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) 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) removeprefix() (in module render_dag) render_config() (in module showyourwork.config) render_dag module replacements (showyourwork.patches.SnakemakeFormatter attribute) RequestError require_access_token() (in module showyourwork.zenodo) restore_trace() (in module showyourwork.exceptions.base) run_snakemake() (in module showyourwork.cli.commands.run_snakemake) RunDirectiveNotAllowedInUserRules S setup() (in module showyourwork.cli.commands.setup) setup_remote() (in module showyourwork.overleaf) should_ignore() (in module render_dag) 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.run_snakemake 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.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