added scripts to build vesper's environment

Author: kaiseriskera

requirements.txt

@@ -0,0 +1,100 @@
+argcomplete==2.0.0
+asttokens==3.0.0
+attrs==25.3.0
+backcall==0.2.0
+beautifulsoup4==4.13.3
+biopython==1.83
+bleach==6.2.0
+Brotli==1.1.0
+certifi==2025.1.31
+cffi==1.16.0
+charset-normalizer==3.4.1
+contourpy==1.2.0
+cssselect2==0.7.0
+cstag==1.0.5
+cstag-cli==1.0.0
+cycler==0.12.1
+decorator==5.2.1
+defusedxml==0.7.1
+distlib==0.3.4
+docopt==0.6.2
+edlib==1.3.9
+executing==2.2.0
+fastjsonschema==2.21.1
+filelock==3.6.0
+fonttools==4.49.0
+html5lib==1.1
+idna==3.10
+importlib_metadata==8.6.1
+importlib_resources==6.1.2
+ipython==8.12.3
+jedi==0.19.2
+Jinja2==3.1.6
+joblib==1.3.2
+jsonschema==4.23.0
+jsonschema-specifications==2024.10.1
+jupyter_client==8.6.3
+jupyter_core==5.7.2
+jupyterlab_pygments==0.3.0
+kaleido==0.2.1
+kiwisolver==1.4.5
+kneebow==1.0.1
+MarkupSafe==3.0.2
+matplotlib==3.8.3
+matplotlib-inline==0.1.7
+mistune==3.1.3
+nbclient==0.10.2
+nbconvert==7.16.6
+nbformat==5.10.4
+numpy==1.26.4
+packaging==21.3
+pandas==2.2.2
+pandocfilters==1.5.1
+Paralleltask==0.2.3
+parso==0.8.4
+pexpect==4.9.0
+pickleshare==0.7.5
+pillow==10.2.0
+pipx==1.1.0
+platformdirs==2.5.2
+plotly==5.19.0
+prompt_toolkit==3.0.50
+psutil==7.0.0
+ptyprocess==0.7.0
+pure_eval==0.2.3
+pyarrow==15.0.2
+pybind11==2.13.6
+pycparser==2.22
+pydyf==0.10.0
+Pygments==2.19.1
+pyparsing==3.0.9
+pyphen==0.15.0
+pysam==0.22.0
+python-dateutil==2.8.2
+Python-Deprecated==1.1.0
+pytz==2024.1
+PyYAML==6.0.1
+pyzmq==26.3.0
+referencing==0.36.2
+requests==2.32.3
+rpds-py==0.24.0
+scipy==1.12.0
+six==1.16.0
+sniffles==2.2
+soupsieve==2.6
+stack-data==0.6.3
+tenacity==8.2.3
+threadpoolctl==3.3.0
+tinycss2==1.3.0
+tornado==6.4.2
+traitlets==5.14.3
+typing_extensions==4.13.0
+tzdata==2024.1
+urllib3==1.26.15
+userpath==1.8.0
+virtualenv==20.14.1
+wcwidth==0.2.13
+webencodings==0.5.1
+yarg==0.1.9
+zipp==3.21.0
+zopfli==0.2.3

setup_vesper_env.py

@@ -0,0 +1,87 @@
+import os
+import subprocess
+import sys
+
+def run_command(command, check=True):
+    """
+    Runs a shell command and handles errors gracefully.
+    """
+    try:
+        print(f"Running: {command}")
+        subprocess.run(command, shell=True, check=check, text=True)
+    except subprocess.CalledProcessError as e:
+        print(f"Error: Command '{command}' failed with exit code {e.returncode}")
+        sys.exit(1)
+
+def patch_cstag_lazy_import():
+    """
+    Patch cstag's to_pdf.py to lazy-import weasyprint only when needed.
+    """
+    to_pdf_path = os.path.join(sys.prefix, "lib", "python3.9", "site-packages", "cstag", "to_pdf.py")
+
+    if not os.path.exists(to_pdf_path):
+        print(f"⚠️  cstag's to_pdf.py not found at {to_pdf_path}. Skipping patch.")
+        return
+
+    with open(to_pdf_path, "r") as f:
+        lines = f.readlines()
+
+    new_lines = []
+    import_removed = False
+    for line in lines:
+        if "from weasyprint import HTML" in line and not import_removed:
+            print("🔧 Removing top-level weasyprint import...")
+            import_removed = True
+            continue
+        new_lines.append(line)
+
+    for i, line in enumerate(new_lines):
+        if line.strip().startswith("def to_pdf("):
+            indent = ' ' * (len(line) - len(line.lstrip()) + 4)
+            new_lines.insert(i + 1, f"{indent}from weasyprint import HTML  # lazy import\n")
+            print("✅ Injected lazy import inside `to_pdf()`.")
+            break
+    else:
+        print("❌ Couldn't find `def to_pdf()` in cstag. No changes made.")
+        return
+
+    with open(to_pdf_path, "w") as f:
+        f.writelines(new_lines)
+
+    print("🎉 Successfully patched cstag to lazy-load weasyprint.")
+
+def main():
+    ### ensure script is running in a virtual environment ###
+    if not hasattr(sys, 'real_prefix') and not (hasattr(sys, 'base_prefix') and sys.base_prefix != sys.prefix):
+        print("Please activate your virtual environment before running this script.")
+        sys.exit(1)
+
+    ### Define installation path ###
+    env_bin = os.path.join(sys.prefix, "bin")
+
+    print(f"Virtual environment detected: {sys.prefix}")
+    print(f"Installing tools into: {env_bin}")
+
+    ### Upgrade pip and install Python dependencies ###
+    run_command("pip install --upgrade pip")
+    run_command("pip install -r requirements.txt")
+
+    ### Install Samtools ###
+    run_command("wget https://github.com/samtools/samtools/releases/download/1.16.1/samtools-1.16.1.tar.bz2")
+    run_command("tar -xvjf samtools-1.16.1.tar.bz2")
+    run_command("cd samtools-1.16.1 && ./configure --prefix=$VIRTUAL_ENV --disable-lzma --without-curses && make && make install && cd ..")
+
+    ### Patch cstag's PDF import ###
+    patch_cstag_lazy_import()
+
+    ### Clean up temporary files ###
+    run_command("rm -f samtools-1.16.1.tar.bz2")
+    run_command("rm -rf samtools-1.16.1")
+
+    ### Verify installations ###
+    run_command(f"{env_bin}/samtools --version")
+
+    print("\nAll tools installed successfully!")
+
+if __name__ == "__main__":
+    main()