Removed pre-compile thermo and trans database files

.github/ISSUE_TEMPLATE/bug_report.md

@@ -1,32 +1,29 @@
 ---
 name: Bug report
-about: Create a report to help us improve
+about: Report a problem to help us improve
 title: "[bug]"
 labels: bug
 assignees: markleader
-
 ---
 
-**Describe the bug**
-A clear and concise description of what the bug is.
-
-- Interface(s) affected: [e.g. Fortran, C, legacy, Python]
-
-- Is this an issue with backwards-compatibility using the legacy interface? If so, paste the the `.inp` problem file, and the relevant output for inspection.
+**Summary**
+A clear, concise description of the bug.
 
-**To Reproduce**
-Steps to reproduce the behavior:
+**Reproduction**
+- Interface: [Fortran | C | Python | legacy]
+- Minimal input / steps (attach .inp if relevant):
+- Command or API call used:
 
 **Expected behavior**
-A clear and concise description of what you expected to happen.
+What you expected to happen.
 
-**Screenshots**
-If applicable, add screenshots to help explain your problem.
+**Actual behavior**
+What happened (include key error messages/output).
 
-**Build architecture (please complete the following information):**
- - OS: [e.g. Mac OS, Windows]
- - Fortran compiler [e.g. gfortran, ifort]
- - Version [e.g. 3.0.0]
+**Environment**
+- OS:
+- CEA version/commit:
+- Compiler or Python version (if relevant):
 
 **Additional context**
-Add any other context about the problem here.
+Anything else helpful (optional).

.github/ISSUE_TEMPLATE/feature_request.md

@@ -1,17 +1,16 @@
 ---
 name: Feature request
-about: Suggest an idea for this project
+about: Suggest an improvement
 title: "[feature]"
 labels: enhancement
 assignees: ''
-
 ---
 
-**Is your feature request related to a problem? Please describe.**
-A clear and concise description of what the problem is. Ex. It is difficult to [...]
+**Problem / use case**
+What’s hard or missing today?
 
-**Describe the solution you'd like**
-A clear and concise description of what you want to happen.
+**Proposed solution**
+What would you like to see?
 
 **Additional context**
-Add any other context or screenshots about the feature request here.
+Examples, references, or alternatives (optional).

.github/pull_request_template.md

@@ -0,0 +1,10 @@
+## Summary
+
+## Changes
+
+## Testing
+- Not run (explain why)
+
+## Compatibility / Numerical behavior
+- [ ] No expected changes to numerical results
+- [ ] Expected changes (explain and provide validation)

.github/workflows/basic_build.yml

@@ -36,12 +36,34 @@ jobs:
         with:
           python-version: "3.12"
 
-      - name: Set up Fortran compiler
+      - name: Set up Fortran compiler (Unix)
+        if: runner.os != 'Windows'
         uses: fortran-lang/setup-fortran@v1
         with:
           compiler: ${{ matrix.toolchain.compiler }}
           version: ${{ matrix.toolchain.version }}
 
+      - name: Set up Fortran compiler (Windows)
+        if: runner.os == 'Windows'
+        run: |
+          # Use pre-installed MinGW on Windows runners to avoid Chocolatey issues
+          # GitHub Actions windows-latest runners include MinGW in C:\ProgramData\chocolatey\lib\mingw\tools\install\mingw64\bin
+          $mingwPath = "C:\ProgramData\chocolatey\lib\mingw\tools\install\mingw64\bin"
+          if (Test-Path $mingwPath) {
+            echo "$mingwPath" | Out-File -FilePath $env:GITHUB_PATH -Encoding utf8 -Append
+            echo "FC=$mingwPath\gfortran.exe" | Out-File -FilePath $env:GITHUB_ENV -Encoding utf8 -Append
+          } else {
+            # Fallback: search for gfortran in common locations
+            $gfortran = Get-Command gfortran -ErrorAction SilentlyContinue
+            if ($gfortran) {
+              echo "FC=$($gfortran.Source)" | Out-File -FilePath $env:GITHUB_ENV -Encoding utf8 -Append
+            } else {
+              Write-Error "gfortran not found on Windows runner"
+              exit 1
+            }
+          }
+        shell: pwsh
+
       - name: Install build tools
         run: |
           python -m pip install --upgrade pip
@@ -52,6 +74,7 @@ jobs:
           git --version
           cmake --version
           ninja --version
+          if command -v gfortran &> /dev/null; then gfortran --version; fi
           if [ -n "${FC}" ]; then "${FC}" --version; fi
 
       - name: Configure

.gitignore

@@ -18,6 +18,7 @@ extern/install
 *.xlsx
 *.pdf
 *.bat
+*.lib
 !sampleThe/*.inp
 !test/main_interface/*.inp
 !test/main_interface/reference_output/*.out

CHANGELOG.md

@@ -0,0 +1,14 @@
+# Changelog
+
+All notable user-visible changes to this project are documented here.
+
+## [Unreleased]
+
+### Changed
+
+### Fixed
+
+### Added
+
+## [3.0.0] – 2025-12-31
+- Initial public release.

CLAUDE.md

@@ -1,13 +1,133 @@
-# AGENTS
-
-This repository is a scientific computing library (CEA). Follow these rules:
-
-- Do NOT modify `thermo.inp` or `trans.inp` unless explicitly instructed.
-- Numerical correctness is paramount; preserve bitwise results and scientific behavior.
-- Avoid algorithmic changes unless explicitly requested.
-- Prefer clarity over cleverness or micro-optimizations.
-- Keep changes small and focused; avoid drive-by formatting or whitespace churn.
-- Maintain backward compatibility for the legacy user base.
-- If numerical behavior might change, call it out and add validation or tests when possible.
-- Respect layer boundaries: Fortran core in `source/`, C bindings in `source/bind/c/`,
-  Python bindings in `source/bind/python/`.
+# CLAUDE.md - AI Agent Instructions for CEA
+
+This repository contains CEA (Chemical Equilibrium with Applications), a NASA scientific computing library for chemical equilibrium calculations. The codebase consists of validated Fortran solvers with C and Python bindings.
+
+## Core Principles
+
+1. **Numerical correctness is paramount** - Preserve bitwise results and scientific behavior
+2. **Backward compatibility matters** - Legacy user base depends on stable behavior
+3. **Clarity over cleverness** - Prefer readable code over micro-optimizations
+4. **Small, focused changes** - One concern per change; avoid bundling unrelated work
+
+## Critical Rules
+
+### Data Files (DO NOT MODIFY)
+- **NEVER** modify `thermo.inp` or `trans.inp` unless explicitly instructed by the user
+- **NEVER** modify `data/thermo.inp` or `data/trans.inp`
+- These files contain validated thermodynamic and transport property databases
+
+### Algorithmic Changes
+- **AVOID** changing solver algorithms unless explicitly requested
+- **AVOID** modifying convergence logic, tolerances, or loop ordering
+- **CALL OUT** any changes that might affect numerical behavior
+- **ADD** validation tests when numerical behavior might change
+
+### Code Quality
+- **AVOID** drive-by formatting or whitespace changes
+- **AVOID** restructuring code for style alone
+- **KEEP** diffs minimal and focused
+- **PRESERVE** existing naming conventions and patterns
+
+## Architecture & Layer Boundaries
+
+```
+source/                 - Fortran core (scientific solvers)
+source/bind/c/          - C ABI bindings (thin adapters)
+source/bind/python/     - Python interface (Cython/NumPy)
+data/                   - Thermodynamic and transport databases
+```
+
+**Respect layer boundaries:**
+- Do not mix Fortran solver changes with binding changes
+- Do not change scientific logic from binding layers
+- Keep C bindings thin (no business logic)
+- Python layer may add Pythonic conveniences but not alter solver behavior
+
+## Build System
+
+- **Build tool**: CMake 3.19+
+- **Languages**: Fortran (core), C (bindings), Python (bindings)
+- **Compilers**: Intel and GNU Fortran are primary targets
+- **Python build**: scikit-build-core with Ninja generator
+- **Presets available**: `core` (Fortran only), `core-c` (Fortran+C), default (all bindings)
+
+### Python Binding Development
+When modifying Python bindings:
+1. Changes to `*.pyx` or `*.pxd` files require rebuild
+2. Editable installs do not auto-rebuild
+3. Rebuild command: `make py-rebuild` (requires Ninja on PATH)
+4. Test command: `pytest source/bind/python/tests`
+5. Ensure `numpy` is installed in the active Python environment
+
+## Testing
+
+- **Run existing tests** before and after changes
+- **Add regression tests** for bug fixes when possible
+- **Add validation tests** for new features
+- **Verify** no unintended behavior changes occur
+
+Test locations:
+- Fortran: Built with `-DCEA_BUILD_TESTING=ON`
+- Python: `pytest source/bind/python/tests`
+- Legacy CLI validation: `test/main_interface/test_main.py`
+- Samples: `samples/` directory contains reference cases
+
+## Common Scenarios
+
+### Bug Fixes
+- Identify root cause before fixing
+- Add regression test if feasible
+- Keep fix minimal and focused
+- Document what was broken and how it's fixed
+
+### Documentation
+- Improvements always welcome
+- Use Markdown or reStructuredText
+- Be technically accurate
+- Avoid marketing language
+- Document assumptions and limitations
+
+### Interface Improvements (C/Python bindings)
+- Allowed and encouraged
+- Do not change solver behavior
+- Add clear docstrings/comments
+- Follow language idioms (Pythonic for Python, etc.)
+
+### Refactoring
+- Discuss with user first for large refactors
+- Prove numerical equivalence
+- Provide before/after comparison
+- Small, incremental refactors preferred
+
+## What to Call Out
+
+**Always explicitly mention if your change involves:**
+- Floating-point arithmetic reordering
+- Loop ordering changes
+- Tolerance or convergence criterion modifications
+- Changes to thermodynamic assumptions
+- Database compilation or access patterns
+- Changes that might affect bitwise reproducibility
+
+## Dependencies
+
+**Core** (Fortran): No external dependencies
+**C bindings**: No additional dependencies
+**Python bindings**: Requires:
+- Cython
+- NumPy
+- scikit-build-core
+- Ninja (build time)
+
+## References
+
+When in doubt, refer to:
+- [CONTRIBUTING.md](CONTRIBUTING.md) - Detailed contribution guidelines
+- [README.md](README.md) - Build and usage instructions
+- `docs/` - Full documentation
+
+## Summary
+
+Priority order: **Numerical correctness > Backward compatibility > Performance > Style**
+
+When uncertain about a change, ask the user first.

CMakeLists.txt

@@ -79,27 +79,56 @@ add_subdirectory(extern/fbasics)
 add_subdirectory(source)
 
 # Build the thermodynamic properties database
-#configure_file(src/thermo.inp thermo.inp COPYONLY)
-#add_custom_target(thermo.lib ALL
-#    COMMAND cea thermo >/dev/null
-#    BYPRODUCTS thermo.lib thermo.out
-#    DEPENDS cea
-#)
+add_custom_command(
+    OUTPUT ${CMAKE_BINARY_DIR}/thermo.lib
+    COMMAND $<TARGET_FILE:cea> --compile-thermo ${CMAKE_SOURCE_DIR}/data/thermo.inp
+    DEPENDS cea ${CMAKE_SOURCE_DIR}/data/thermo.inp
+    WORKING_DIRECTORY ${CMAKE_BINARY_DIR}
+    COMMENT "Compiling thermodynamic database from thermo.inp"
+)
 
 # Build the transport properties database
-#configure_file(src/trans.inp trans.inp COPYONLY)
-#add_custom_target(trans.lib ALL
-#    COMMAND cea trans >/dev/null
-#    BYPRODUCTS trans.lib trans.out
-#    DEPENDS cea
-#)
+add_custom_command(
+    OUTPUT ${CMAKE_BINARY_DIR}/trans.lib
+    COMMAND $<TARGET_FILE:cea> --compile-trans ${CMAKE_SOURCE_DIR}/data/trans.inp
+    DEPENDS cea ${CMAKE_SOURCE_DIR}/data/trans.inp
+    WORKING_DIRECTORY ${CMAKE_BINARY_DIR}
+    COMMENT "Compiling transport database from trans.inp"
+)
+
+# Create a custom target that depends on both database files
+add_custom_target(compile_databases ALL
+    DEPENDS ${CMAKE_BINARY_DIR}/thermo.lib ${CMAKE_BINARY_DIR}/trans.lib
+)
+
+if(PROJECT_IS_TOP_LEVEL)
+    add_custom_command(TARGET compile_databases POST_BUILD
+        COMMAND ${CMAKE_COMMAND} -E copy_if_different
+                ${CMAKE_BINARY_DIR}/thermo.lib ${CMAKE_SOURCE_DIR}/data/thermo.lib
+        COMMAND ${CMAKE_COMMAND} -E copy_if_different
+                ${CMAKE_BINARY_DIR}/trans.lib ${CMAKE_SOURCE_DIR}/data/trans.lib
+        COMMAND ${CMAKE_COMMAND} -E make_directory
+                ${CMAKE_SOURCE_DIR}/source/bind/python/cea/data
+        COMMAND ${CMAKE_COMMAND} -E copy_if_different
+                ${CMAKE_BINARY_DIR}/thermo.lib
+                ${CMAKE_SOURCE_DIR}/source/bind/python/cea/data/thermo.lib
+        COMMAND ${CMAKE_COMMAND} -E copy_if_different
+                ${CMAKE_BINARY_DIR}/trans.lib
+                ${CMAKE_SOURCE_DIR}/source/bind/python/cea/data/trans.lib
+        COMMENT "Copying compiled databases to source data directory"
+    )
+endif()
 
 
 #-----------------------------------------------------------------------
 # Installation
 #-----------------------------------------------------------------------
 install(
-    FILES data/thermo.lib data/trans.lib
+    FILES ${CMAKE_BINARY_DIR}/thermo.lib ${CMAKE_BINARY_DIR}/trans.lib
+    DESTINATION ${CMAKE_INSTALL_DATAROOTDIR}/cea
+)
+install(
+    FILES ${CMAKE_BINARY_DIR}/thermo.lib ${CMAKE_BINARY_DIR}/trans.lib
     DESTINATION ${CMAKE_INSTALL_PREFIX}/data
 )
 install(EXPORT cea-config