feat: Migrate all formulas from python@3.12 to python@3.13

Migrates taskrepo, rxiv-maker, and folder2md4llms to python@3.13.
This resolves CI test failures caused by python@3.12 deprecation issues.

Changes:
- Update all formulas to depend on python@3.13
- Update venv creation to use python3.13
- Simplify test workflows (remove workarounds)
- Re-enable all test workflows

Author: paxcalpt

…rkflows/test-folder2md4llms.yml.disabled .github/workflows/test-folder2md4llms.yml.github/workflows/test-folder2md4llms.yml.disabled renamed to .github/workflows/test-folder2md4llms.yml .github/workflows/test-folder2md4llms.yml.disabled renamed to .github/workflows/test-folder2md4llms.yml

@@ -42,32 +42,9 @@ jobs:
       - name: Install taskrepo
         env:
           HOMEBREW_NO_INSTALL_CLEANUP: 1
-          HOMEBREW_NO_INSTALLED_DEPENDENTS_CHECK: 1
         run: |
           echo "Installing taskrepo..."
-          # Try installing formula (may have python@3.12 deprecation warnings)
-          brew install --build-from-source "henriqueslab/formulas/taskrepo" 2>&1 | tee install.log || {
-            # Check if it's just the deprecation warning issue
-            if grep -q "missing keywords: :date, :because" install.log; then
-              echo "⚠️  Python deprecation warning detected (known Homebrew issue)"
-              # Try installing with --force-bottle for python
-              brew uninstall --ignore-dependencies taskrepo 2>/dev/null || true
-              HOMEBREW_NO_INSTALL_FROM_API=1 brew install --build-from-source "henriqueslab/formulas/taskrepo" || {
-                if brew list "taskrepo" &>/dev/null; then
-                  echo "✓ Formula installed despite warnings"
-                else
-                  echo "❌ Formula installation failed"
-                  exit 1
-                fi
-              }
-            elif brew list "taskrepo" &>/dev/null; then
-              echo "⚠️  Formula installed with warnings (expected for Python venvs)"
-            else
-              echo "❌ Formula installation failed"
-              cat install.log
-              exit 1
-            fi
-          }
+          brew install --build-from-source "henriqueslab/formulas/taskrepo"
 
       - name: Test taskrepo
         run: |

…b/workflows/test-rxiv-maker.yml.disabled .github/workflows/test-rxiv-maker.yml.github/workflows/test-rxiv-maker.yml.disabled renamed to .github/workflows/test-rxiv-maker.yml .github/workflows/test-rxiv-maker.yml.disabled renamed to .github/workflows/test-rxiv-maker.yml

@@ -6,13 +6,13 @@ class Folder2md4llms < Formula
   sha256 "5b4ad2f89c821f8d5178645a549517d4a5bcd9510cc17d9e8b937f07a52f6a08"
   license "MIT"
 
-  depends_on "python@3.12"
+  depends_on "python@3.13"
   depends_on "libmagic"
 
   def install
     # Create a virtual environment inside libexec
     venv = libexec/"venv"
-    system Formula["python@3.12"].opt_bin/"python3.12", "-m", "venv", venv
+    system Formula["python@3.13"].opt_bin/"python3.13", "-m", "venv", venv
 
     # Install the package with all dependencies
     # Binary wheels are allowed for faster installation

.github/workflows/test-taskrepo.yml

@@ -7,13 +7,13 @@ class RxivMaker < Formula
 
   depends_on "gh"
   depends_on "git"
-  depends_on "python@3.12"
+  depends_on "python@3.13"
   depends_on "texlive"
   depends_on "latexdiff"
 
   def install
     venv = libexec/"venv"
-    system Formula["python@3.12"].opt_bin/"python3.12", "-m", "venv", venv
+    system Formula["python@3.13"].opt_bin/"python3.13", "-m", "venv", venv
     system venv/"bin/pip", "install", "-v", "--ignore-installed",
            build.head? ? "git+." : "."
     bin.install_symlink venv/"bin/rxiv"

.github/workflows/test-taskrepo.yml.disabled

@@ -6,14 +6,14 @@ class Taskrepo < Formula
   sha256 "8506d0673698c8c7d45e9dac889b93a1b976953d0b0becedb45abe951f7b29eb"
   license "MIT"
 
-  depends_on "python@3.12"
+  depends_on "python@3.13"
   depends_on "git"
   depends_on "gh"
 
   def install
     # Create a virtual environment inside libexec
     venv = libexec/"venv"
-    system Formula["python@3.12"].opt_bin/"python3.12", "-m", "venv", venv
+    system Formula["python@3.13"].opt_bin/"python3.13", "-m", "venv", venv
 
     # Install the package with all dependencies
     # Binary wheels are allowed for faster installation