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Issue title

Python: requests without timeout

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Severity Rule Title File:line
HIGH MINED108 [MINED108] `self.to_frontend_params` used but never assigned in __init__: Method `to_dict… server/workflow/engine_runtime.py:165
HIGH MINED108 [MINED108] `self.is_total` used but never assigned in __init__: Method `label` of class `… extensions/cohp-analysis/catgo_cohp/io.…:189
HIGH MINED108 [MINED108] `self.app` used but never assigned in __init__: Method `__call__` of class `_S… server/main.py:452
HIGH MINED034 [MINED034] Python Subprocess Shell True: subprocess(..., shell=True) enables command inje… server/workflow/engines/sella.py:103
HIGH SEC078 [SEC078] Python: requests without timeout: requests.get/post without a timeout will hang … server/run_cp2k_sp.py:53
HIGH MINED021 [MINED021] Path Traversal Os Join: os.path.join(user_dir, filename) where filename can co… server/plugin_loader.py:17
HIGH SEC135 [SEC135] Auth/permission check missing on AI-generated endpoint: Mutating HTTP endpoint g… server/catgo/routers/cohp.py:58
HIGH SEC135 [SEC135] Auth/permission check missing on AI-generated endpoint: Mutating HTTP endpoint g… server/catgo/routers/chgcar.py:58
HIGH SEC135 [SEC135] Auth/permission check missing on AI-generated endpoint: Mutating HTTP endpoint g… server/catgo/routers/atomate2.py:23
HIGH MINED004 [MINED004] Weak Crypto: MD5/SHA1/DES/RC4 used for security context (not just checksums). scripts/patch-linuxdeploy-sidecars.mjs:46
HIGH MINED012 [MINED012] Curl Pipe Bash: curl ... | sh / bash — runs unverified network code. scripts/setup.mjs:81
HIGH MINED012 [MINED012] Curl Pipe Bash: curl ... | sh / bash — runs unverified network code. scripts/agent-dev.mjs:42
HIGH SEC103 [SEC103] LDAP injection — non-constant search filter: User input concatenated into an LDA… scripts/parse_gaussian.py:46
HIGH SEC103 [SEC103] LDAP injection — non-constant search filter: User input concatenated into an LDA… plugins/cp2k-dos-reader/tool.py:200
HIGH SEC103 [SEC103] LDAP injection — non-constant search filter: User input concatenated into an LDA… plugins/cp2k-dos-reader/plugin.py:196
HIGH SEC029 [SEC029] Server-Side Request Forgery (SSRF) — outbound HTTP from user input: Outbound HTT… server/catgo/routers/mcp_sse.py:4
HIGH SEC029 [SEC029] Server-Side Request Forgery (SSRF) — outbound HTTP from user input: Outbound HTT… server/catgo/cli/server_link.py:19
HIGH SEC029 [SEC029] Server-Side Request Forgery (SSRF) — outbound HTTP from user input: Outbound HTT… extensions/vscode/src/sidecar.ts:42
HIGH SEC085 [SEC085] JS: child_process.exec with non-literal: child_process.exec with user-derived in… scripts/setup.mjs:60
HIGH SEC085 [SEC085] JS: child_process.exec with non-literal: child_process.exec with user-derived in… scripts/build-agent-sidecar.mjs:67
HIGH SEC085 [SEC085] JS: child_process.exec with non-literal: child_process.exec with user-derived in… extensions/vscode/src/optimade-backend.…:128
HIGH MINED001 [MINED001] Bare Except Pass: except: pass or except Exception: pass — silently swallows e… server/catgo/cli/_legacy.py:83
HIGH MINED001 [MINED001] Bare Except Pass: except: pass or except Exception: pass — silently swallows e… server/catgo/calculators/base.py:57
HIGH MINED001 [MINED001] Bare Except Pass: except: pass or except Exception: pass — silently swallows e… extensions/dos-analysis/catgo_dos/orbit…:112
HIGH MINED009 [MINED009] Floats For Money: Variable named price/amount/cost typed as float instead of D… server/catgo/models/cohp.py:71
HIGH MINED009 [MINED009] Floats For Money: Variable named price/amount/cost typed as float instead of D… extensions/dos-analysis/catgo_dos/dband…:259
HIGH SEC128 [SEC128] Async function without await — fire-and-forget Promise (AI mistake): Async call … server/catgo/cli/__init__.py:150
HIGH SEC128 [SEC128] Async function without await — fire-and-forget Promise (AI mistake): Async call … extensions/dos-analysis/catgo_dos/orbit…:119
HIGH SEC128 [SEC128] Async function without await — fire-and-forget Promise (AI mistake): Async call … energy_diagram/examples/keyboard_demo.py:66
HIGH SEC040 [SEC040] innerHTML XSS — template literal with server-supplied data: Setting .innerHTML w… extensions/vscode/vite.webview.config.ts:17
HIGH SEC040 [SEC040] innerHTML XSS — template literal with server-supplied data: Setting .innerHTML w… extensions/vscode/src/optimade-backend.…:165
HIGH SEC040 [SEC040] innerHTML XSS — template literal with server-supplied data: Setting .innerHTML w… desktop/main.ts:15
HIGH MINED003 [MINED003] Rust Unwrap In Prod: .unwrap() panics if None/Err. Acceptable in tests; risky … crates/catgo-graph/src/tools/file_write…:107
HIGH MINED003 [MINED003] Rust Unwrap In Prod: .unwrap() panics if None/Err. Acceptable in tests; risky … crates/catgo-graph/src/runtime/lifecycl…:144
HIGH DKR006 Dockerfile pipes a remote script into a shell Dockerfile:29
HIGH MINED115 [MINED115] Action `j178/prek-action` pinned to mutable ref `@v1`: `uses: j178/prek-action… .github/workflows/lint.yml:27
HIGH MINED115 [MINED115] Action `denoland/setup-deno` pinned to mutable ref `@v2`: `uses: denoland/setu… .github/workflows/lint.yml:22
HIGH MINED115 [MINED115] Action `actions/checkout` pinned to mutable ref `@v5`: `uses: actions/checkout… .github/workflows/lint.yml:19
HIGH MINED126 [MINED126] Workflow container/services image `mcr.microsoft.com/playwright:v1.58.0-noble`… .github/workflows/test.yml:73
HIGH MINED115 [MINED115] Action `dtolnay/rust-toolchain` pinned to mutable ref `@stable`: `uses: dtolna… .github/workflows/test.yml:92
HIGH MINED115 [MINED115] Action `actions/setup-node` pinned to mutable ref `@v4`: `uses: actions/setup-… .github/workflows/test.yml:86
HIGH MINED115 [MINED115] Action `pnpm/action-setup` pinned to mutable ref `@v4`: `uses: pnpm/action-set… .github/workflows/test.yml:83
HIGH MINED115 [MINED115] Action `actions/checkout` pinned to mutable ref `@v4`: `uses: actions/checkout… .github/workflows/test.yml:80
HIGH MINED115 [MINED115] Action `dtolnay/rust-toolchain` pinned to mutable ref `@stable`: `uses: dtolna… .github/workflows/test.yml:34
HIGH MINED115 [MINED115] Action `actions/setup-node` pinned to mutable ref `@v4`: `uses: actions/setup-… .github/workflows/test.yml:28
HIGH MINED115 [MINED115] Action `pnpm/action-setup` pinned to mutable ref `@v4`: `uses: pnpm/action-set… .github/workflows/test.yml:25
HIGH MINED115 [MINED115] Action `actions/checkout` pinned to mutable ref `@v4`: `uses: actions/checkout… .github/workflows/test.yml:22
HIGH MINED115 [MINED115] Action `tauri-apps/tauri-action` pinned to mutable ref `@v0.6`: `uses: tauri-a… .github/workflows/tauri-build.yml:185
HIGH MINED115 [MINED115] Action `swatinem/rust-cache` pinned to mutable ref `@v2`: `uses: swatinem/rust… .github/workflows/tauri-build.yml:174
HIGH MINED115 [MINED115] Action `oven-sh/setup-bun` pinned to mutable ref `@v2`: `uses: oven-sh/setup-b… .github/workflows/tauri-build.yml:141
HIGH MINED115 [MINED115] Action `dtolnay/rust-toolchain` pinned to mutable ref `@stable`: `uses: dtolna… .github/workflows/tauri-build.yml:136
HIGH MINED115 [MINED115] Action `dtolnay/rust-toolchain` pinned to mutable ref `@stable`: `uses: dtolna… .github/workflows/tauri-build.yml:113
HIGH MINED115 [MINED115] Action `conda-incubator/setup-miniconda` pinned to mutable ref `@v3`: `uses: c… .github/workflows/tauri-build.yml:96
HIGH MINED115 [MINED115] Action `actions/setup-node` pinned to mutable ref `@v4`: `uses: actions/setup-… .github/workflows/tauri-build.yml:90
HIGH MINED115 [MINED115] Action `pnpm/action-setup` pinned to mutable ref `@v4`: `uses: pnpm/action-set… .github/workflows/tauri-build.yml:87
HIGH MINED115 [MINED115] Action `actions/checkout` pinned to mutable ref `@v4`: `uses: actions/checkout… .github/workflows/tauri-build.yml:70
HIGH MINED115 [MINED115] Action `actions/upload-artifact` pinned to mutable ref `@v4`: `uses: actions/u… .github/workflows/vsix-publish.yml:127
HIGH MINED115 [MINED115] Action `dtolnay/rust-toolchain` pinned to mutable ref `@stable`: `uses: dtolna… .github/workflows/vsix-publish.yml:41
HIGH MINED115 [MINED115] Action `actions/setup-node` pinned to mutable ref `@v5`: `uses: actions/setup-… .github/workflows/vsix-publish.yml:29
HIGH MINED115 [MINED115] Action `pnpm/action-setup` pinned to mutable ref `@v4`: `uses: pnpm/action-set… .github/workflows/vsix-publish.yml:27
HIGH MINED115 [MINED115] Action `actions/checkout` pinned to mutable ref `@v5`: `uses: actions/checkout… .github/workflows/vsix-publish.yml:24
HIGH MINED118 [MINED118] Dockerfile FROM `python:3.11-slim-bookworm` not pinned by digest: `FROM python… deploy/hpc/Dockerfile:43
HIGH MINED118 [MINED118] Dockerfile FROM `node:20-bookworm-slim` not pinned by digest: `FROM node:20-bo… deploy/hpc/Dockerfile:12
HIGH MINED131 [MINED131] pre-commit hook `https://github.com/pre-commit/mirrors-eslint` pinned to mutab… .pre-commit-config.yaml:57
HIGH MINED131 [MINED131] pre-commit hook `https://github.com/igorshubovych/markdownlint-cli` pinned to … .pre-commit-config.yaml:42
HIGH MINED131 [MINED131] pre-commit hook `https://github.com/codespell-project/codespell` pinned to mut… .pre-commit-config.yaml:33
HIGH MINED131 [MINED131] pre-commit hook `https://github.com/pre-commit/pre-commit-hooks` pinned to mut… .pre-commit-config.yaml:6
HIGH MINED118 [MINED118] Dockerfile FROM `python:3.11-slim-bookworm` not pinned by digest: `FROM python… Dockerfile:70
HIGH MINED118 [MINED118] Dockerfile FROM `node:22-bookworm-slim` not pinned by digest: `FROM node:22-bo… Dockerfile:14
HIGH MINED122 [MINED122] package.json dep `@catgo/ferrox-wasm` pulled from URL/Git: `dependencies.@catg… package.json:1
HIGH JRN009 Secret-like setting is echoed into a password input value src/lib/structure/ServerPane.svelte:1492
HIGH JRN009 Secret-like setting is echoed into a password input value src/lib/mobile/MobileConnect.svelte:445
HIGH JRN009 Secret-like setting is echoed into a password input value src/lib/chat/ChatPane.svelte:1207
HIGH JRN009 Secret-like setting is echoed into a password input value src/lib/ConnectDialog.svelte:466
HIGH MINED112 [MINED112] FastAPI POST /{workflow_id}/recheck-jobs has no auth: Handler `api_recheck_job… server/catgo/routers/workflow.py:469
HIGH MINED112 [MINED112] FastAPI POST /{workflow_id}/reset has no auth: Handler `api_reset_workflow` is… server/catgo/routers/workflow.py:435
HIGH MINED112 [MINED112] FastAPI POST /{workflow_id}/steps/{step_id}/retry has no auth: Handler `api_re… server/catgo/routers/workflow.py:418
HIGH MINED112 [MINED112] FastAPI PUT /{workflow_id}/steps/{step_id} has no auth: Handler `api_update_st… server/catgo/routers/workflow.py:397
HIGH MINED112 [MINED112] FastAPI DELETE /{workflow_id} has no auth: Handler `api_delete_workflow` is re… server/catgo/routers/workflow.py:388
HIGH MINED112 [MINED112] FastAPI PUT /{workflow_id} has no auth: Handler `api_update_workflow` is regis… server/catgo/routers/workflow.py:371
HIGH MINED112 [MINED112] FastAPI POST /engine-defs/custom has no auth: Handler `create_custom_engine` i… server/catgo/routers/workflow.py:336
HIGH MINED112 [MINED112] FastAPI POST /from-template/{template_id} has no auth: Handler `api_create_fro… server/catgo/routers/workflow.py:305
HIGH MINED112 [MINED112] FastAPI POST /quickbuild has no auth: Handler `api_quickbuild` is registered w… server/catgo/routers/workflow.py:238
HIGH MINED112 [MINED112] FastAPI POST / has no auth: Handler `api_create_workflow` is registered with r… server/catgo/routers/workflow.py:191
HIGH MINED112 [MINED112] FastAPI POST /pending-update has no auth: Handler `push_pending_workflow_updat… server/catgo/routers/workflow.py:165
HIGH MINED112 [MINED112] FastAPI POST /import-flow has no auth: Handler `import_flow` is registered wit… server/catgo/routers/quacc.py:55
HIGH MINED112 [MINED112] FastAPI POST /upload has no auth: Handler `trajectory_upload` is registered wi… server/catgo/routers/trajectory_stream.…:580
HIGH MINED112 [MINED112] FastAPI POST /import-flow has no auth: Handler `import_flow` is registered wit… server/catgo/routers/atomate2.py:24
HIGH MINED112 [MINED112] FastAPI POST /refresh has no auth: Handler `refresh_plugins` is registered wit… server/catgo/routers/plugins.py:604
HIGH MINED112 [MINED112] FastAPI POST /install/upload has no auth: Handler `install_plugin_upload` is r… server/catgo/routers/plugins.py:563
HIGH MINED112 [MINED112] FastAPI DELETE /{plugin_name} has no auth: Handler `uninstall_plugin` is regis… server/catgo/routers/plugins.py:550
HIGH MINED112 [MINED112] FastAPI POST /{plugin_name}/disable has no auth: Handler `disable_plugin` is r… server/catgo/routers/plugins.py:525
HIGH MINED112 [MINED112] FastAPI POST /{plugin_name}/enable has no auth: Handler `enable_plugin` is reg… server/catgo/routers/plugins.py:500
HIGH MINED112 [MINED112] FastAPI POST /analyzers/{analyzer_id}/run has no auth: Handler `run_analyzer` … server/catgo/routers/plugins.py:432
HIGH MINED112 [MINED112] FastAPI POST /readers/upload has no auth: Handler `upload_to_reader` is regist… server/catgo/routers/plugins.py:206
HIGH MINED112 [MINED112] FastAPI POST /report/upload-text has no auth: Handler `upload_report_text` is … server/catgo/routers/vasp.py:224
HIGH MINED112 [MINED112] FastAPI POST /report/upload has no auth: Handler `upload_report_file` is regis… server/catgo/routers/vasp.py:192
HIGH MINED112 [MINED112] FastAPI POST /generate has no auth: Handler `generate_vasp_inputs_endpoint` is… server/catgo/routers/vasp.py:130
HIGH MINED112 [MINED112] FastAPI POST /parse-structure has no auth: Handler `parse_structure` is regist… server/catgo/routers/vasp.py:67
HIGH SEC013 [SEC013] Path Traversal — User Input in File Path: User-controlled input used in file pat… server/workflow/engines/sella.py:215
HIGH SEC020 [SEC020] Secret Printed to Logs: Debug or diagnostic code appears to print a credential-b… server/catgo/routers/materials_project.…:29
MED MINED109 [MINED109] Mutable default argument in `run_tool` (dict): `def run_tool(... = []/{}/set()… server/catgo/routers/tools.py:60
MED MINED111 [MINED111] Bare except continues silently: Bare `except:` (or `except Exception:`) that r… scripts/cp2k_dos.py:254
MED MINED111 [MINED111] Bare except continues silently: Bare `except:` (or `except Exception:`) that r… server/main.py:521
MED SEC087 [SEC087] JS: weak Math.random for crypto: Math.random() is not cryptographically secure; … src/site/plot-utils.ts:135
MED SEC136 [SEC136] AI-typical over-broad exception handler swallowing all errors: Catch-all excepti… server/catgo/routers/tools.py:81
MED SEC034 [SEC034] Log Injection / Log Forging — unsanitized user input in log: User input is logge… server/catgo/routers/moire.py:193
MED ERR001 [ERR001] Silent Exception Swallowing: Silently swallowing all exceptions hides bugs. Even… server/catgo/mcp_tools/plugin_tools.py:108
MED ERR001 [ERR001] Silent Exception Swallowing: Silently swallowing all exceptions hides bugs. Even… server/catgo/mcp_tools/helpers.py:198
MED ERR001 [ERR001] Silent Exception Swallowing: Silently swallowing all exceptions hides bugs. Even… server/catgo/calculators/base.py:112
MED SEC045 [SEC045] eval()/exec() on stored or user-supplied data: eval() and exec() on data — even … server/catgo/tools/sandbox.py:191
MED SEC045 [SEC045] eval()/exec() on stored or user-supplied data: eval() and exec() on data — even … server/catgo/plugins/sandbox.py:236
MED SEC045 [SEC045] eval()/exec() on stored or user-supplied data: eval() and exec() on data — even … extensions/vscode/src/optimade-backend.…:128
MED COMP001 [COMP001] High cognitive complexity: Function `parse_orbital_spec` has cognitive complexi… extensions/dos-analysis/catgo_dos/orbit…:78
MED DKR001 Docker final stage has no non-root USER deploy/hpc/Dockerfile.base:5
MED DKR001 Docker final stage has no non-root USER deploy/hpc/Dockerfile:43
MED DKR001 Docker final stage has no non-root USER Dockerfile:70
MED AGT007 localStorage write failures are swallowed silently desktop/state/sidebar-state.svelte.ts:52
MED AGT007 localStorage write failures are swallowed silently desktop/lib/popout-manager.ts:14
MED WEB003 Public web service has no security.txt .well-known/security.txt
MED DKR014 Dockerfile copies broad context with incomplete .dockerignore Dockerfile:44
MED AGT012 Agent control bridge may listen on a network interface without visible auth server/main.py:1
MED AGT015 Remote install command pipes network code directly to a shell deploy/web/install.sh:7
MED AGT015 Remote install command pipes network code directly to a shell deploy/web/INSTALL.md:10
MED AGT015 Remote install command pipes network code directly to a shell .github/workflows/vsix-publish.yml:47
MED AGT015 Remote install command pipes network code directly to a shell .github/workflows/test.yml:39
MED AGT015 Remote install command pipes network code directly to a shell .github/workflows/tauri-test-build.yml:90
MED AGT015 Remote install command pipes network code directly to a shell .github/workflows/ios-build.yml:82
MED AGT015 Remote install command pipes network code directly to a shell .github/workflows/hpc-bundle.yml:57
MED SEC005 [SEC005] Command Injection Risk: Unsafe shell execution or eval of user input. server/workflow/engines/sella.py:103
LOW COMP001 [COMP001] High cognitive complexity: Function `_on_text_input` has cognitive complexity 1… energy_diagram/energydiagram/interactio…:153
LOW COMP001 [COMP001] High cognitive complexity: Function `_on_editor_action` has cognitive complexit… energy_diagram/energydiagram/interactio…:21
LOW AIC003 Duplicated implementation block across source files server/catgo/utils/scheduler_base.py:13
LOW AIC003 Duplicated implementation block across source files server/catgo/tools/builtin/vasp_readers…:14
LOW AIC003 Duplicated implementation block across source files server/catgo/routers/reticular.py:27
LOW AIC003 Duplicated implementation block across source files server/catgo/routers/reticular.py:25
LOW AIC003 Duplicated implementation block across source files server/catgo/routers/qe.py:115
LOW AIC003 Duplicated implementation block across source files server/catgo/routers/qe.py:20
LOW AIC003 Duplicated implementation block across source files server/catgo/routers/optimize_ws.py:97
LOW AIC003 Duplicated implementation block across source files server/catgo/routers/mofdb.py:18
LOW AIC003 Duplicated implementation block across source files server/catgo/routers/mcp_sse.py:22
LOW AIC003 Duplicated implementation block across source files server/catgo/routers/cube.py:16
LOW AIC003 Duplicated implementation block across source files server/catgo/calculators/xtb_cli.py:22
LOW AIC003 Duplicated implementation block across source files plugins/lammps-workflow/tool.py:43
LOW AIC003 Duplicated implementation block across source files plugins/cp2k-dos-reader/tool.py:2
LOW AIC003 Duplicated implementation block across source files plugins/bond-histogram/tool.py:10
LOW AIC003 Duplicated implementation block across source files extensions/rust/src/wasm_nanoscroll.rs:36
LOW AIC003 Duplicated implementation block across source files extensions/rust/src/pbc.rs:75
LOW AIC003 Duplicated implementation block across source files extensions/rust/src/mof/rac.rs:368
LOW AIC003 Duplicated implementation block across source files extensions/rust/src/mof/rac.rs:338
LOW AIC003 Duplicated implementation block across source files extensions/rust/src/mof/mod.rs:115
LOW AIC003 Duplicated implementation block across source files extensions/rust/src/crystal_nn.rs:536
LOW AIC003 Duplicated implementation block across source files extensions/rust/src/coordination.rs:331
LOW AIC003 Duplicated implementation block across source files extensions/rust/src/batch.rs:272
LOW AIC003 Duplicated implementation block across source files desktop/components/ExportSaveDialog.sve…:138
LOW AIC003 Duplicated implementation block across source files crates/catgo-graph/src/tools/vasp.rs:20
LOW AIC003 Duplicated implementation block across source files crates/catgo-graph/src/tools/stats.rs:107
LOW AIC003 Duplicated implementation block across source files crates/catgo-graph/src/runtime/schedule…:152
LOW AIC003 Duplicated implementation block across source files crates/catgo-graph/src/runtime/lifecycl…:121
LOW AIC003 Duplicated implementation block across source files crates/catgo-graph/src/runtime/engine.rs:618
LOW AIC003 Duplicated implementation block across source files crates/catgo-graph/src/graph/validate.rs:149
LOW WEB001 Public web app has no robots.txt robots.txt
LOW WEB002 Public web app has no sitemap sitemap.xml
LOW DKR008 .dockerignore misses sensitive defaults .dockerignore
LOW DKR012 Dockerfile keeps pip download cache Dockerfile:103
LOW WEB008 Public docs site has no llms.txt llms.txt
LOW DKC010 Compose service lacks no-new-privileges hardening docker-compose.yml:7
LOW DKC006 Compose service does not declare a runtime user docker-compose.yml:7
LOW WEB011 Public web app has no humans.txt humans.txt
INFO MINED054 [MINED054] Ts As Any: Casting to any (as any) bypasses type checking entirely. vite-plugin-agent-bridge.ts:109
INFO MINED052 [MINED052] Ts Any Typed: : any used as type annotation. Defeats TypeScript type safety. vite-plugin-agent-bridge.ts:123
INFO MINED067 [MINED067] Python Requests No Timeout: requests.get/post/etc. without timeout= can hang f… server/run_cp2k_sp.py:53
INFO MINED076 [MINED076] Catch And Reraise Noop: except X: raise X — adds no value, hides traceback if … server/catgo/utils/hpc_client.py:69
INFO MINED077 [MINED077] Python Open No Context: fp = open(path) outside with-block leaks file handles. server/catgo/utils/local_connection.py:149
INFO MINED077 [MINED077] Python Open No Context: fp = open(path) outside with-block leaks file handles. server/catgo/tools/sandbox.py:190
INFO MINED072 [MINED072] Python Pass Only Class: class Foo: pass — stub waiting to be filled in. server/catgo/tools/discovery.py:17
INFO MINED049 [MINED049] Print Pii: Logging password/token/email/ssn directly to stdout. server/catgo/routers/materials_project.…:29
INFO MINED062 [MINED062] Python Dataclass No Fields: @dataclass over an empty class — unfinished model. server/catgo/cli/hpc_link.py:46
INFO MINED062 [MINED062] Python Dataclass No Fields: @dataclass over an empty class — unfinished model. extensions/dos-analysis/catgo_dos/pdos.…:68
INFO MINED062 [MINED062] Python Dataclass No Fields: @dataclass over an empty class — unfinished model. extensions/dos-analysis/catgo_dos/dband…:23
INFO MINED064 [MINED064] Python Input Call: input() blocks for stdin. Inappropriate in services. energy_diagram/examples/test.py:17
INFO MINED064 [MINED064] Python Input Call: input() blocks for stdin. Inappropriate in services. energy_diagram/examples/keyboard_demo.py:65
INFO MINED050 [MINED050] Stub Only Function: Function declared but body is just pass, return None, rais… extensions/dos-analysis/catgo_dos/orbit…:113
INFO MINED050 [MINED050] Stub Only Function: Function declared but body is just pass, return None, rais… examples/plugins/lennard-jones-calculat…:43
INFO MINED050 [MINED050] Stub Only Function: Function declared but body is just pass, return None, rais… energy_diagram/energydiagram/interactio…:200
INFO MINED045 [MINED045] Ts Non Null Assertion: x! asserts not null - bypasses null checks - TypeError … src/scripts/fetch-elem-images.ts:62
INFO MINED045 [MINED045] Ts Non Null Assertion: x! asserts not null - bypasses null checks - TypeError … extensions/vscode/scripts/sync-config.ts:25
INFO MINED045 [MINED045] Ts Non Null Assertion: x! asserts not null - bypasses null checks - TypeError … desktop/pane-utils.ts:102
INFO MINED044 [MINED044] Js Console Log Prod: console.log left in code. Should be replaced with logger … desktop/sidebar/rename-save-dialogs.sve…:42
INFO MINED044 [MINED044] Js Console Log Prod: console.log left in code. Should be replaced with logger … desktop/settings.ts:29
INFO MINED044 [MINED044] Js Console Log Prod: console.log left in code. Should be replaced with logger … desktop/main.ts:31
INFO MINED055 [MINED055] Npm Install No Lockfile: Production image runs npm install (resolves new versi… scripts/build-server.sh:54
INFO MINED055 [MINED055] Npm Install No Lockfile: Production image runs npm install (resolves new versi… deploy/hpc/conda/setup-catgo.sh:66
INFO MINED043 [MINED043] Http Not Https: Hardcoded http:// (not localhost) for endpoints that handle cr… extensions/catrender-wasm/src/lib.rs:22
INFO MINED043 [MINED043] Http Not Https: Hardcoded http:// (not localhost) for endpoints that handle cr… deploy/hpc/catgo-job.sh:154
INFO MINED043 [MINED043] Http Not Https: Hardcoded http:// (not localhost) for endpoints that handle cr… deploy/hpc/bundle/catgo-job.sh:154
INFO MINED059 [MINED059] Rust Expect In Prod: .expect(...) panics same as unwrap with a custom message. extensions/catrender-wasm/src/types.rs:222
INFO MINED059 [MINED059] Rust Expect In Prod: .expect(...) panics same as unwrap with a custom message. crates/catgo-graph/src/tools/stats.rs:109
INFO MINED059 [MINED059] Rust Expect In Prod: .expect(...) panics same as unwrap with a custom message. crates/catgo-graph/src/tools/http_bridg…:69
INFO MINED066 [MINED066] Rust Panic Macro: panic!() unwinds the stack. Use Result for recoverable error… crates/catgo-graph/src/runtime/lifecycl…:102
Reset to top 5 200 findings available (after auto-suppression of test files + won't-fix)

Issue body (markdown)

## Code-quality scan: `Hello-QM/catgo-LRG`

**Score: 75/100 (A)**  ·  297 findings  ·  scanned 2026-06-05 14:56 UTC  ·  571,269 LOC

| Severity | Count |
|---|---|
| CRITICAL | 23 |
| HIGH | 102 |
| MEDIUM | 29 |
| LOW | 39 |

📊 [Full filterable report](https://repobility.com/scan/6b565384-68f5-42ad-a5cf-2addef33ce3d/)  ·  ![scorecard](https://repobility.com/scan/6b565384-68f5-42ad-a5cf-2addef33ce3d/report.png?v=1780671389-s2)

### Top findings

1. **HIGH** `MINED108` — `self.to_frontend_params` used but never assigned in __init__
   `server/workflow/engine_runtime.py:165` · ✓ Repobility
2. **HIGH** `MINED108` — `self.is_total` used but never assigned in __init__
   `extensions/cohp-analysis/catgo_cohp/io.py:189` · ✓ Repobility
3. **HIGH** `MINED108` — `self.app` used but never assigned in __init__
   `server/main.py:452` · ✓ Repobility
4. **HIGH** `MINED034` — Python Subprocess Shell True
   `server/workflow/engines/sella.py:103` · CWE-78 · ✓ Repobility
5. **HIGH** `SEC078` — Python: requests without timeout
   `server/run_cp2k_sp.py:53` · A05:2021 Security Misconfiguration

---

**Security note**: this issue is public. If any flagged finding is a real, exploitable vulnerability, please redirect to your `SECURITY.md` policy or open a [private security advisory](https://docs.github.com/en/code-security/security-advisories/guidance-on-reporting-and-writing-information-about-vulnerabilities/privately-reporting-a-security-vulnerability) instead. We're happy to close this and re-submit privately.

---

_Filed automatically. Close this issue if not useful — we won't refile. Full report: https://repobility.com/scan/6b565384-68f5-42ad-a5cf-2addef33ce3d/_
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Could not determine 'Hello-QM/catgo-LRG' star count (GitHub API rate-limited or unreachable). When in doubt about repo size, prefer opening a focused PR or a discussion rather than an issue.
Already filed
116/317 findings (37%) on this scan are already flagged as test-file, won't-fix, or suppressed. The scan is too noisy to file as a single issue. Curate down to specific actionable findings, or address the FP source first.
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