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Functions1,796 in github.com/K-Dense-AI/scientific-agent-skills

⨍ Functions 1,796◇ Types & classes 89
↓ 95 callersMethodsearch
Search PubMed and return PMIDs. Args: query: Search query max_results: Maximum number of results
skills/citation-management/scripts/search_pubmed.py:36
↓ 54 callersFunctioninfo
Print a progress message to stderr-friendly stdout with a marker.
skills/scanpy/scripts/_common.py:16
↓ 45 callersMethodclose
Clean up environment resources.
skills/stable-baselines3/scripts/custom_env_template.py:216
↓ 25 callersMethod_log
Log message if verbose mode is enabled.
skills/infographics/scripts/generate_infographic_ai.py:341
↓ 24 callersMethod_log
Log message if verbose mode is enabled.
skills/venue-templates/scripts/generate_schematic_ai.py:153
↓ 24 callersMethod_log
Log message if verbose mode is enabled.
skills/scholar-evaluation/scripts/generate_schematic_ai.py:153
↓ 24 callersMethod_log
Log message if verbose mode is enabled.
skills/scientific-slides/scripts/generate_schematic_ai.py:153
↓ 24 callersMethod_log
Log message if verbose mode is enabled.
skills/scientific-writing/scripts/generate_schematic_ai.py:153
↓ 24 callersMethod_log
Log message if verbose mode is enabled.
skills/hypothesis-generation/scripts/generate_schematic_ai.py:153
↓ 24 callersMethod_log
Log message if verbose mode is enabled.
skills/research-lookup/scripts/generate_schematic_ai.py:153
↓ 24 callersMethod_log
Log message if verbose mode is enabled.
skills/clinical-reports/scripts/generate_schematic_ai.py:153
↓ 24 callersMethod_log
Log message if verbose mode is enabled.
skills/clinical-decision-support/scripts/generate_schematic_ai.py:153
↓ 24 callersMethod_log
Log message if verbose mode is enabled.
skills/latex-posters/scripts/generate_schematic_ai.py:153
↓ 24 callersMethod_log
Log message if verbose mode is enabled.
skills/pptx-posters/scripts/generate_schematic_ai.py:153
↓ 24 callersMethod_log
Log message if verbose mode is enabled.
skills/treatment-plans/scripts/generate_schematic_ai.py:153
↓ 24 callersMethod_log
Log message if verbose mode is enabled.
skills/peer-review/scripts/generate_schematic_ai.py:153
↓ 24 callersMethod_log
Log message if verbose mode is enabled.
skills/markitdown/scripts/generate_schematic_ai.py:153
↓ 24 callersMethod_log
Log message if verbose mode is enabled.
skills/citation-management/scripts/generate_schematic_ai.py:153
↓ 24 callersMethod_log
Log message if verbose mode is enabled.
skills/scientific-schematics/scripts/generate_schematic_ai.py:153
↓ 24 callersMethod_log
Log message if verbose mode is enabled.
skills/literature-review/scripts/generate_schematic_ai.py:153
↓ 20 callersMethoderror
(self, msg: str)
skills/bulk-rnaseq/scripts/validate_samplesheet.py:43
↓ 20 callersFunctionfail
(message)
skills/pacsomatic/scripts/run_pacsomatic.py:39
↓ 19 callersMethod_log
Log message if verbose mode is enabled.
skills/scientific-slides/scripts/generate_slide_image_ai.py:178
↓ 19 callersFunctiondie
Print an error and exit.
skills/scanpy/scripts/_common.py:21
↓ 19 callersFunctionredact
(text: str)
skills/autoskill/scripts/redact.py:37
↓ 16 callersFunctionshell_literal
Quote a sanitized value for use in a generated bash assignment.
skills/deeptools/scripts/workflow_generator.py:68
↓ 15 callersFunctionwrite_output
(text)
skills/research-lookup/research_lookup.py:480
↓ 15 callersFunctionwrite_output
(text)
skills/research-lookup/scripts/research_lookup.py:480
↓ 14 callersFunctionconfigure_scanpy
Apply consistent scanpy settings and return the scanpy module. Note: autosave is left off by default because the toolkit scripts pass explici
skills/scanpy/scripts/_common.py:35
↓ 14 callersFunctionload_anndata
Load an AnnData object, dispatching on the file extension / layout. Supported inputs: * ``.h5ad`` -> sc.read_h5ad *
skills/scanpy/scripts/_common.py:53
↓ 13 callersMethodto_dict
(self)
skills/timesfm-forecasting/scripts/check_system.py:102
↓ 11 callersFunction_save
(path, data)
skills/arbor/scripts/tree.py:68
↓ 11 callersFunction_tree_path
(run_dir)
skills/arbor/scripts/tree.py:50
↓ 11 callersFunctionrun
(config, *, start_time, end_time, out_dir, screenpipe_client, backend, embedder, skills_dir, s
skills/autoskill/scripts/run.py:68
↓ 11 callersFunctionsave_anndata
Write an AnnData object to .h5ad, creating parent dirs as needed.
skills/scanpy/scripts/_common.py:88
↓ 10 callersFunction_evt
(ts: int, app: str, title: str = "", text: str = "")
skills/autoskill/tests/test_cluster.py:4
↓ 10 callersFunctionadd_io_args
Attach the standard input/output/figdir arguments to an argparse parser.
skills/scanpy/scripts/_common.py:96
↓ 10 callersFunctioninfo
(message)
skills/pacsomatic/scripts/run_pacsomatic.py:44
↓ 9 callersFunction_load_tree
(run_dir)
skills/arbor/scripts/tree.py:76
↓ 9 callersFunctionformat_value
Format DICOM values for display.
skills/pydicom/scripts/extract_metadata.py:23
↓ 9 callersFunctionsanitize_path
Return a shell-safe path-like value for generated workflow scripts.
skills/deeptools/scripts/workflow_generator.py:37
↓ 9 callersFunctionsynthesize
(cluster, top_k_skills, backend)
skills/autoskill/scripts/synthesize.py:57
↓ 8 callersFunctionfetch_window
(client, start_time, end_time, page_size=50, token=None)
skills/autoskill/scripts/fetch_window.py:4
↓ 8 callersFunctionseverity_badge
(sev: str)
scan_skills.py:46
↓ 7 callersFunction_base_config
()
skills/autoskill/tests/test_run.py:50
↓ 7 callersFunction_cluster
()
skills/autoskill/tests/test_synthesize.py:18
↓ 7 callersFunction_make_client
(handler)
skills/autoskill/tests/test_fetch_window.py:7
↓ 7 callersFunction_randomize
(df, randomize, seed)
skills/experimental-design/scripts/doe_designs.py:43
↓ 7 callersFunction_top_k
()
skills/autoskill/tests/test_synthesize.py:27
↓ 7 callersFunction_write_skill
(root: Path, name: str, description: str)
skills/autoskill/tests/test_run.py:13
↓ 7 callersMethodconvert
Convert PDF to images using PyMuPDF.
skills/scientific-slides/scripts/pdf_to_images.py:48
↓ 7 callersMethodlookup
Perform a research lookup, routing to the best backend. Parallel Chat API is used by default. Perplexity sonar-pro-search is used onl
skills/research-lookup/research_lookup.py:408
↓ 7 callersFunctionwarn
(message)
skills/pacsomatic/scripts/run_pacsomatic.py:48
↓ 7 callersMethodwarn
(self, msg: str)
skills/bulk-rnaseq/scripts/validate_samplesheet.py:46
↓ 6 callersFunction_config
(tmp_path: Path)
skills/autoskill/tests/test_doctor.py:6
↓ 6 callersFunction_fake_result
(**overrides)
skills/exa-search/tests/test_exa_search.py:38
↓ 6 callersFunction_load_run
(run_dir)
skills/arbor/scripts/tree.py:80
↓ 6 callersFunction_node
(tree, node_id)
skills/arbor/scripts/tree.py:90
↓ 6 callersFunction_screenpipe_client_with_events
(events)
skills/autoskill/tests/test_run.py:19
↓ 6 callersFunction_sev_str
(obj)
scan_pr_skills.py:35
↓ 6 callersFunction_stamp
(node)
skills/arbor/scripts/tree.py:115
↓ 6 callersFunction_write_skill
(root: Path, name: str, description: str)
skills/autoskill/tests/test_e2e.py:27
↓ 6 callersFunctioncheck
(config, *, skills_dir, screenpipe_probe, llm_probe)
skills/autoskill/scripts/doctor.py:47
↓ 6 callersFunctionload_tree
Load tree from file.
skills/etetoolkit/scripts/tree_operations.py:24
↓ 6 callersFunctionmake_backend
(config)
skills/autoskill/scripts/backends.py:50
↓ 6 callersFunctionpromote
(proposed_path, skills_dir, name)
skills/autoskill/scripts/promote.py:14
↓ 5 callersFunction_append_xml
(xml_path: Path, root_tag: str, content: str)
skills/docx/scripts/comment.py:86
↓ 5 callersFunction_decode_two_level
Map a -1/+1 coded matrix to real (low/high) units per factor.
skills/experimental-design/scripts/doe_designs.py:31
↓ 5 callersFunction_load_script
Load one of the scripts as a module regardless of cwd.
skills/exa-search/tests/test_exa_search.py:28
↓ 5 callersFunction_ocr
(ts: str, app: str, title: str, text: str)
skills/autoskill/tests/test_e2e.py:51
↓ 5 callersMethod_parse_id_value
(self, val: str, base: int = 16)
skills/pptx/scripts/office/validators/docx.py:251
↓ 5 callersMethod_parse_id_value
(self, val: str, base: int = 16)
skills/docx/scripts/office/validators/docx.py:251
↓ 5 callersMethod_parse_id_value
(self, val: str, base: int = 16)
skills/xlsx/scripts/office/validators/docx.py:251
↓ 5 callersMethod_read_reference
(self, filename)
skills/open-notebook/scripts/test_open_notebook_skill.py:247
↓ 5 callersFunction_stage_proposed_skill
(proposed_root: Path, kind: str, name: str, body: str = "---\nname: s\ndescription:
skills/autoskill/tests/test_promote.py:8
↓ 5 callersFunctionfetch
(url: str)
skills/hugging-science/scripts/fetch_catalog.py:95
↓ 5 callersFunctionsegment_sessions
(events, idle_gap_seconds, min_session_seconds)
skills/autoskill/scripts/cluster.py:4
↓ 5 callersFunctiontop_k_matches
(query, skills, embedder, k)
skills/autoskill/scripts/match_skills.py:38
↓ 4 callersFunction_ancestors
Path from node up to (and including) root, nearest first.
skills/arbor/scripts/tree.py:101
↓ 4 callersFunction_events_two_sessions
(app="Chrome")
skills/autoskill/tests/test_run.py:56
↓ 4 callersFunction_mock_client
(handler, base_url="")
skills/autoskill/tests/test_backends.py:7
↓ 4 callersFunction_run_path
(run_dir)
skills/arbor/scripts/tree.py:54
↓ 4 callersMethod_run_with_mock
(self, argv)
skills/exa-search/tests/test_exa_search.py:145
↓ 4 callersFunction_seed_skills_dir
A tiny but representative slice of the real skills/ layout.
skills/autoskill/tests/test_e2e.py:33
↓ 4 callersFunctionadd_divider
(ax, label_top=True)
skills/timesfm-forecasting/examples/covariates-forecasting/demo_covariates.py:163
↓ 4 callersFunctioncluster_sessions
(sessions, min_cluster_size)
skills/autoskill/scripts/cluster.py:35
↓ 4 callersFunctionhas_any_command
(names)
skills/pacsomatic/scripts/run_pacsomatic.py:69
↓ 4 callersFunctionload_skill_descriptions
(skills_dir)
skills/autoskill/scripts/match_skills.py:19
↓ 4 callersFunctionsample_size
Solve for required sample size. For per-group tests (t_ind, two_proportions) returns n PER GROUP. For anova returns TOTAL n across all groups
skills/statistical-power/scripts/power.py:186
↓ 4 callersFunctionsimulate_power
Estimate power at sample size `n`. gen_and_test(n, rng) -> bool : build a dataset of size n under the assumed effect, run the planned ana
skills/statistical-power/scripts/simulate_power.py:50
↓ 4 callersMethodsummary
Print summary statistics for all resources.
skills/simpy/scripts/resource_monitor.py:224
↓ 3 callersFunction_base_config
()
skills/autoskill/tests/test_e2e.py:138
↓ 3 callersMethod_check_script
(self, filename)
skills/open-notebook/scripts/test_open_notebook_skill.py:315
↓ 3 callersFunction_children
(tree, node_id)
skills/arbor/scripts/tree.py:97
↓ 3 callersFunction_clean_sample_name
Strip common aligner suffixes/extensions from a file or column name.
skills/bulk-rnaseq/scripts/build_counts_matrix.py:41
↓ 3 callersFunction_dir
(run_dir)
skills/arbor/scripts/tree.py:46
↓ 3 callersFunction_find_elements
(root, tag: str)
skills/pptx/scripts/office/helpers/merge_runs.py:44
↓ 3 callersFunction_find_elements
(root, tag: str)
skills/docx/scripts/office/helpers/merge_runs.py:44
↓ 3 callersFunction_find_elements
(root, tag: str)
skills/xlsx/scripts/office/helpers/merge_runs.py:44
↓ 3 callersFunction_is_run
(node)
skills/pptx/scripts/office/helpers/merge_runs.py:154
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