scitex 2.13.0__py3-none-any.whl → 2.15.1__py3-none-any.whl

scitex/scholar/docs/to_claude/guidelines/project/IMPORTANT-project-management-org.org

@@ -1,161 +0,0 @@
-# Timestamp: "2025-05-30 05:03:49 (ywatanabe)"
-# File: /ssh:ywatanabe@sp:/home/ywatanabe/.dotfiles/.claude/to_claude/guidelines/project/IMPORTANT-project-management-org.org
-
-#+TITLE: Project Management Rules
-#+AUTHOR: ywatanabe
-#+DATE: 2025-05-20 05:43:47
-
-Project management is conducted under =./project_management= directory.
-
-* Core Files and Locations
-- Original plan: =./project_management/USER_PLAN.md= (DO NOT EDIT)
-- Updated plans: =./project_management/CLAUDE_PLAN.org= (Use this as a persistent memory)
-- Progress tracking (Org): =./project_management/progress-<title>.org=
-- Progress tracking (Mermaid) : =./project_management/progress-<title>.mmd=
-- Memory across sessions: =./project_management/next_steps.md=
-
-* Progress Format
-#+BEGIN_SRC org
-#+TITLE: Project Title
-
-* Goal 1: Description
-** TODO Milestone 1
-*** DONE Task 1
-**** `./path/to/file/which/justify/the/completion/example.py`
-**** `./path/to/file/which/justify/the/completion/example.jpg`
-**** `./path/to/file/which/justify/the/completion/example.csv`
-*** TODO Task 2
-
-* Goal 2: Description  
-** DONE Milestone 2
-*** DONE Task 3
-*** DONE Task 4
-#+END_SRC
-
-* Visual Progress Management using Mermaid Diagram
-- =./project_management/progress-<title>.mmd=
-  - Mermaid diagram definition file reflecting =./project_management/progress-<title>.org=
-  - Use tags as well
-  - Use TD layout
-  - Understand the hierarchy and summarize into core elements
-  - Summarize up to most-important 7 elements
-- =./project_management/progress-<title>.svg=
-  - SVG file created from the mermaid file
-- =./project_management/progress-<title>.gif=
-  - GIF image created from the SVG file
-
-** Rendering Tool
-Use =.claude/bin/render_mermaid.sh /path/to/mermaid/file.mmd=
-
-** Example
-#+BEGIN_SRC mermaid
-graph TD
-    subgraph Legend
-        Z1[Todo]:::todo
-        Z2[In Progress]:::inProgress
-        Z3[Done]:::done
-        Z4[Directory]:::directory
-    end
-    
-    subgraph Project Structure
-    subgraph PD[Project Description]
-        PJNAME[Project Name]:::done
-        PJGOALS[Goals]:::done
-    end
-    
-    subgraph PDIR[Project Directory]
-        Root["\/workspace\/projects\/000-sample-project"]:::directory
-        Config[config/]:::directory
-        Data[data/]:::directory
-        Scripts[scripts/]:::directory
-        Results[results/]:::directory
-        Resources[resources/]:::directory
-        Env[.env/]:::directory
-        Git[.git/]:::directory
-        Requirements[requirements.txt/]:::directory
-        Log[Log.txt/]:::directory
-        PM[project_management.mmd]:::directory
-    end
-    end
-    
-    subgraph Execution Flow
-    subgraph Step
-        D[Compile Context]:::done
-        E[Generate Elisp]:::inProgress
-        F[Execute Elisp]:::todo
-        G{Success?}:::todo
-    end
-    
-    subgraph "Logging, Version Control, and State Update"
-        H[Log Success]:::todo
-        I[Log Error]:::todo
-        J{Milestone?}:::todo
-        K[Git Commit]:::todo
-        L[Log Only]:::todo
-        M{Goal Met?}:::todo
-        N[Update Project_States]:::todo
-    end
-    end
-    
-    subgraph PMFLOW[Project Management Flow]
-        MS1[Milestone 1]:::done
-        MS2[Milestone 2]:::inProgress
-        
-    subgraph Tasks M1
-        T1[task1]:::done
-        T2[task2]:::done
-    end
-    
-    subgraph Tasks M2
-        T3[task1]:::done
-        T4[task2]:::todo
-    end
-    end
-    
-    Start[Start]:::starttag --> PD
-    PD --> PDIR
-    PM --> PMFLOW
-    PMFLOW --> PM
-    PDIR --> D
-    D --> E --> F --> G
-    G -- Yes --> H
-    G -- No --> I
-    H --> J
-    J -- Yes --> K
-    J -- No --> L
-    K --> M
-    I --> L
-    L --> M
-    M -- No --> N
-    N --> Root
-    M -- Yes --> End[End]:::endtag
-    PJGOALS --> PMFLOW
-    MS1 --> T1
-    MS1 --> T2
-    MS2 --> T3
-    MS2 --> T4
-    
-    classDef starttag fill:#cce5ff,stroke:#333,stroke-width:2px;
-    classDef done fill:#9f9,stroke:#333,stroke-width:2px;
-    classDef inProgress fill:#ff9,stroke:#333,stroke-width:2px;
-    classDef todo fill:#fff,stroke:#333,stroke-width:2px;
-    classDef directory fill:#efe,stroke:#333,stroke-width:1px;
-    classDef endtag fill:#fcc,stroke:#333,stroke-width:2px;
-    class Root,Config,Data,Scripts,Results,Resources directory;
-#+END_SRC
-
-* Your Understanding Check
-Did you understand the guideline? If yes, please say:
-=CLAUDE UNDERSTOOD: <THIS FILE PATH HERE>=
-
-# EOF
-
-# EOF
-
-# EOF
-
-# EOF
-
-# EOF
-
-# EOF

scitex/scholar/docs/to_claude/guidelines/project/IMPORTANT-tools.md

@@ -1,10 +0,0 @@
-<!-- ---
-!-- Timestamp: 2025-05-29 02:29:41
-!-- Author: ywatanabe
-!-- File: /ssh:ywatanabe@sp:/home/ywatanabe/.dotfiles/.claude/to_claude/guidelines/project/IMPORTANT-tools.md
-!-- --- -->
-
-## Use tools prepared for agents
-`.claude/to_claude/bin/**/*.sh`
-
-<!-- EOF -->

scitex/scholar/docs/to_claude/guidelines/project/IMPORTANT-understand-message-in-filename.md

@@ -1,12 +0,0 @@
-<!-- ---
-!-- Timestamp: 2025-06-01 00:38:19
-!-- Author: ywatanabe
-!-- File: /home/ywatanabe/.dotfiles/.claude/to_claude/guidelines/project/IMPORTANT-understand-message-in-filename.md
-!-- --- -->
-
-# Prompt as part of filename
-Users may change filenames to indicate tasks. Understand the user's intent and perform the task accordingly.
-- In that case, users start file name from `-`: e.g., `./path/to/-refactor-this-cluttered-script.py` to indicate users want agents to refactor the file
-- After executing the task, rename path by removing prompt in path 
-
-<!-- EOF -->

scitex/scholar/docs/to_claude/guidelines/project/general.md

@@ -1,7 +0,0 @@
-<!-- ---
-!-- Timestamp: 2025-06-07 02:32:40
-!-- Author: ywatanabe
-!-- File: /ssh:ywatanabe@sp:/home/ywatanabe/.claude/to_claude/guidelines/project/general.md
-!-- --- -->
-
-<!-- EOF -->

scitex/scholar/docs/to_claude/guidelines/project/report.md

@@ -1,50 +0,0 @@
-<!-- ---
-!-- Timestamp: 2025-05-19 10:21:26
-!-- Author: ywatanabe
-!-- File: /ssh:ywatanabe@sp:/home/ywatanabe/.dotfiles/.claude/to_claude/guidelines/guidelines_reporting_rules.md
-!-- --- -->
-
-## Report using Org
-- Summarize the current repository as a report
-- INCLUDE DIAGRAMS, FIGURES, AND TABLES EFFECTIVELY
-- `./project_management/reports/progress-report-YYYY-MMDD-<title>.org`
-- Once org file created, convert to pdf using pandoc:
-  ```bash
-  pandoc -f org -t pdf -o "./project_management/reports/progress-report-YYYY-MMDD-<title>.pdf" "./project_management/reports/progress-report-YYYY-MMDD-<title>.org"
-  ```
-
-- pandoc and pdflatex might be available via:
-  - `module load Pandoc/3.1.2 texlive/20230313`
-
-## Report Format
-
-```org
-# Timestamp: "YYYY-MM-DD HH:mm:ss (ywatanabe)"
-# File: <path-to-projects>/<project-id>-<project-name>/reports/YYYY-MMDD-HHmmss-<title>-report.org
-
-#+STARTUP: showall
-#+OPTIONS: toc:nil num:nil
-#+TITLE: <title>
-#+DATE: YYYY-MMDD-HHmmss
-
-  - Project Directory
-<path-to-projects>/<project-id>-<project-name>/
-
-  - Header 1
-
-  -  - Header 2
-description:
-
-#+ATTR_HTML: :width 600px
-[[file:/path/to/filename.xxx]]
-
-
-  - PDF
-[[file:<path-to-projects>/<project-id>-<project-name>/reports/YYYY-MMDD-HHmmss-<title>/report.pdf]]
-```
-
-## Your Understanding Check
-Did you understand the guideline? If yes, please say:
-`CLAUDE UNDERSTOOD: <THIS FILE PATH HERE>`
-
-<!-- EOF -->

scitex/scholar/docs/to_claude/guidelines/project/timeline-gantt-chart.md

@@ -1,49 +0,0 @@
-<!-- ---
-!-- Timestamp: 2025-06-10 07:13:06
-!-- Author: ywatanabe
-!-- File: /home/ywatanabe/.dotfiles/.claude/to_claude/guidelines/project/timeline-gantt-chart.md
-!-- --- -->
-
-Timeline Gantt charts are excellent tools for planning, directing, and communicating. Therefore, we encourage incorporating this technique into progress management.
-
-Absolute time is not always important; instead, relative time or the visualization of project progression is most important. Therefore, timestamps are not necessarily accurate. You may check git history, but precision is not strictly required.
-
-Embed `git commit hash` to each element. If embedding numbers will clutter output figure, just include comments in mermaid files.
-
-Timeline should be saved as:
-    `./project_management/timeline-<timestamp>.mmd`
-    `./project_management/timeline-<timestamp>.png`
-
-# Timeline Gantt Chart Format
-
-``` mermaid
-gantt
-    dateFormat  YYYY-MM-DD
-    title       Emacs Claude Code Project Timeline
-    
-    section Core Components
-    Term Claude Mode            :done,    term_mode,     2025-04-01, 2025-04-15
-    Auto Response System        :done,    auto_resp,     2025-04-10, 2025-04-30
-    State Detection             :done,    state_det,     2025-04-15, 2025-05-05
-    Visual Aids                 :done,    visual_aids,   2025-04-25, 2025-05-10
-    Interaction Limits          :active,  inter_limits,  2025-05-10, 2025-05-30
-    
-    section Advanced Features
-    Yank As File                :done,    yank_file,     2025-04-20, 2025-05-15
-    Buffer Management           :done,    buffer_mgmt,   2025-05-01, 2025-05-18
-    Templates                   :active,  templates,     2025-05-15, 2025-06-05
-    Notifications               :active,  notifs,        2025-05-20, 2025-06-10
-    
-    section Infrastructure
-    Variables & Configuration   :done,    vars_config,   2025-04-01, 2025-04-20
-    Testing Framework           :done,    testing,       2025-04-05, 2025-05-10
-    Documentation               :active,  docs,          2025-05-01, 2025-06-15
-    
-    section Bug Fixes
-    Auto Response Timer         :done,    timer_fix,     2025-05-05, 2025-05-12
-    Dashboard Buffer Visibility :done,    dash_fix,      2025-05-08, 2025-05-14
-    Debug Message Control       :done,    debug_fix,     2025-05-12, 2025-05-18
-    Initial Waiting Detection   :done,    waiting_fix,   2025-05-15, 2025-05-20
-```
-
-<!-- EOF -->

scitex/scholar/docs/to_claude/guidelines/python/CHECKLIST.md

@@ -1,51 +0,0 @@
-<!-- ---
-!-- Timestamp: 2025-06-01 03:30:44
-!-- Author: ywatanabe
-!-- File: /home/ywatanabe/.dotfiles/.claude/to_claude/guidelines/python/IMPORTANT_CHECKLIST.md
-!-- --- -->
-
-# Checklist for project completion
-  [ ] Are all matplotlib run in "Agg" mode and figures are saved instead of shown?
-- [ ] Is the directory structure appropriate?
-  - [ ] For scientific project:
-    - [ ] `./scripts` instead of `./src`
-  - [ ] For pip package:
-    - [ ] `./src` instead of `./scripts`
-    - [ ] `./pyproject.toml`
-        - [ ] Does `uv pip install -e .` work?
-    - [ ] `./MANIFEST.in`
-  - [ ] Both types:
-    - [ ] `./README.md`
-    - [ ] `./CONTRIBUTING.md`
-    - [ ] `./LICENSE`
-    - [ ] `./docs`
-    - [ ] `./examples`
-      - [ ] Is the structure mirroring `./src`?
-      - [ ] Are all example scripts strictly following the scitex framework?
-      - [ ] Are all example scripts produces outputs and logs?
-      - [ ] Are all example scripts successfully run?
-      - [ ] Is there problems stem from external packages?
-      - [ ] Used `./examples/run_examples.sh`
-      - [ ] Used `./examples/sync_examples_with_source.sh`
-      - [ ] Used `./run_examples.sh`
-    - [ ] `./tests`
-      - [ ] Is the structure mirroring `./src`?
-      - [ ] Are all example scripts strictly following the scitex framework?
-        - [ ] But to reduce dependency, non-scitex framework is acceptable for tests.
-      - [ ] Are all example scripts produces outputs and logs?
-      - [ ] Are all example scripts successfully run?
-      - [ ] Is there problems stem from external packages?
-      - [ ] Used `./examples/run_examples.sh`
-      - [ ] Used `./examples/sync_examples_with_source.sh`
-      - [ ] Used `./run_tests.sh`
-    - [ ] `./project_management`
-      - [ ] `./project_management/BULLETIN-BOARD.md`
-        - [ ] Is obsolete information deleted?
-      - [ ] `./project_management/bug-reports/{,solved}`
-        - [ ] Are they updated?
-      - [ ] `./project_management/feature-requests/{,solved}`
-        - [ ] Are they updated?
-    - [ ] pytest.ini
-    - [ ] __init__.py
-
-<!-- EOF -->

scitex/scholar/docs/to_claude/guidelines/python/HOW-TO-DEBUG-with-MULTIPLE_AGENTS.md

@@ -1,191 +0,0 @@
-<!-- ---
-!-- Timestamp: 2025-08-31 05:04:43
-!-- Author: ywatanabe
-!-- File: /home/ywatanabe/.claude/to_claude/guidelines/python/HOW-TO-DEBUG-with-MULTIPLE_AGENTS.md
-!-- --- -->
-
-### Session Management
-```bash
-# Create session
-screen -dmS debug_$ISSUE_ID
-
-# Send commands
-screen -S debug_$ISSUE_ID -X stuff "python script.py\n"
-
-# Capture output with history
-screen -S debug_$ISSUE_ID -X hardcopy -h /tmp/debug_capture.txt
-
-# Clean up
-screen -S debug_$ISSUE_ID -X quit
-```
-
-### Live Debugging
-```bash
-# List current code
-screen -S debug_$ISSUE_ID -X stuff "l\n"
-
-# Inspect variables
-screen -S debug_$ISSUE_ID -X stuff "pp locals()\n"
-
-# Continue execution
-screen -S debug_$ISSUE_ID -X stuff "c\n"
-```
-
-## CIPDB Integration
-
-### Agent-Specific Breakpoints
-```python
-import cipdb
-import os
-
-# Only DebuggerAgent stops here
-cipdb.set_trace(os.getenv("AGENT_ID") == "DebuggerAgent")
-
-# ID-based conditional breakpoints
-cipdb.set_trace(id="validation_error")
-cipdb.set_trace(id="db_connection")
-cipdb.set_trace(id="auth_failure")
-```
-
-### Environment Control
-```bash
-# Agent identification
-export AGENT_ID=DebuggerAgent
-
-# Selective breakpoint activation
-export CIPDB_IDS=validation_error,auth_failure
-
-# Disable all breakpoints
-export CIPDB_ID=false
-```
-
-## Multi-Agent Workflow
-
-### 1. Issue Identification
-```bash
-# Initial error capture
-screen -dmS error_scan
-screen -S error_scan -X stuff "python failing_script.py\n"
-sleep 2
-screen -S error_scan -X hardcopy -h /tmp/initial_error.txt
-grep "Traceback\|Error" /tmp/initial_error.txt
-```
-
-### 2. Breakpoint Insertion
-File: problematic_script.py
-```python
-# Add conditional breakpoints at suspected locations
-import cipdb
-
-def validate_input(data):
-    cipdb.set_trace(id="input_validation")
-    # validation logic here
-
-def database_query(sql):
-    cipdb.set_trace(id="db_query") 
-    # database code here
-```
-
-### 3. Targeted Debugging
-```bash
-# Activate specific breakpoints
-export CIPDB_IDS=input_validation
-export AGENT_ID=DebuggerAgent
-
-# Start debugging session
-screen -dmS debug_input
-screen -S debug_input -X stuff "python problematic_script.py\n"
-sleep 1
-
-# Capture debugger state
-screen -S debug_input -X hardcopy -h /tmp/debug_state.txt
-tail -20 /tmp/debug_state.txt
-```
-
-### 4. State Analysis
-```bash
-# Extract current location
-grep "^> " /tmp/debug_state.txt | tail -1
-
-# Check variable states
-screen -S debug_input -X stuff "pp vars()\n"
-sleep 0.5
-screen -S debug_input -X hardcopy -h /tmp/vars.txt
-```
-
-### 5. Hypothesis Testing
-```bash
-# Modify variables in debugger
-screen -S debug_input -X stuff "data['field'] = 'corrected_value'\n"
-
-# Continue and observe
-screen -S debug_input -X stuff "c\n"
-sleep 2
-screen -S debug_input -X hardcopy -h /tmp/result.txt
-```
-
-## Output Parsing
-
-### Session Status Check
-```bash
-# Check if debugger is active
-tail -1 /tmp/debug_capture.txt | grep -q "ipdb>" && echo "In debugger"
-
-# Extract current file and line
-grep "^> " /tmp/debug_capture.txt | tail -1 | awk '{print $2 ":" $3}'
-```
-
-### Error Detection
-```bash
-# Check for exceptions
-grep -i "traceback\|error\|exception" /tmp/debug_capture.txt
-
-# Success indicators
-grep -i "completed\|success\|passed" /tmp/debug_capture.txt
-```
-
-## Agent Coordination
-
-### TestAgent Setup
-```bash
-export AGENT_ID=TestAgent
-# TestAgent inserts breakpoints but doesn't stop
-cipdb.set_trace(id="test_failure", condition=False)
-```
-
-### DebuggerAgent Activation
-```bash
-export AGENT_ID=DebuggerAgent  
-export CIPDB_IDS=test_failure
-# DebuggerAgent activates TestAgent's breakpoints
-```
-
-## Best Practices
-
-1. Session Naming
-   - Use: debug_${ISSUE_ID}_${TIMESTAMP}
-   - Avoid conflicts between concurrent debugging
-
-2. Timing
-   - Add sleep 0.5-2s after commands before capture
-   - Screen needs time to process
-
-3. Cleanup
-   - Run screen -wipe periodically
-   - Set CIPDB_ID=false in production
-
-4. Breakpoint IDs
-   - Use descriptive names: auth_failure, db_timeout
-   - Document ID purposes in code comments
-
-## Integration Benefits
-
-- No wrapper complexity - direct screen usage
-- CIPDB enables selective debugging per agent
-- Multiple agents can debug same codebase simultaneously  
-- Full observability through screen captures
-- Simple environment variable control
-
-The combination provides powerful debugging without architectural overhead.
-
-<!-- EOF -->

scitex/scholar/docs/to_claude/guidelines/python/Machine-Learning.md

@@ -1,15 +0,0 @@
-<!-- ---
-!-- Timestamp: 2025-06-01 03:00:13
-!-- Author: ywatanabe
-!-- File: /home/ywatanabe/.dotfiles/.claude/to_claude/guidelines/python/IMPORTANT-Machine-Learning.md
-!-- --- -->
-
-# WHen accuracy is 100%
-It will be highly likely the application has issues
-1. Check Data Pipeline
-2. Check data leakage
-3. Check what is evaluated
-4. Is the result reasonable?
-5. What is the root causes and how to fix if it is a problem?
-
-<!-- EOF -->

scitex/scholar/docs/to_claude/guidelines/python/NOT-FULL-PYTEST-BUT-PARTIAL-PYTEST.md

@@ -1,21 +0,0 @@
-<!-- ---
-!-- Timestamp: 2025-08-31 05:10:07
-!-- Author: ywatanabe
-!-- File: /home/ywatanabe/.claude/to_claude/guidelines/python/NOT-FULL-PYTEST-BUT-PARTIAL-PYTEST.md
-!-- --- -->
-
-## Do not run `pytest tests/`
-Running pytest for all tests takes quite long time (like more than 10 min) and need multiple CPU cores to run. So, in this project, `running full-test` is responsible for the user. Specifically, the user runs the following command regularly so that please check the `test-full-log-latest.txt` with carefully checking the timestamp
-
-``` bash
-LOG_FILE=test-full-log-"$(date +%Y-%m-%d-%H:%M:%S)".txt
-make test-full | tee "$LOG_FILE" 2>&1
-ln -sfr "$LOG_FILE" test-full-log-latest.txt
-tail -n 1 "$LOG_FILE"
-# ==== 154 failed, 1712 passed, 27 skipped, 43 warnings in 391.44s (0:06:31) =====make: *** [Makefile:76: test-full] Error 1
-```
-
-## Run pytest partically: `pytest tests/specific/directory
-However, you may want to check pytest soon after your edition. In that case, please run pytest for only specific, minimal tests to minimize time used.
-
-<!-- EOF -->