Revert "Never install dxtbx into conda_base/ when running under libtbx (

#474)" (#483)

This reverts commit cbe9fa9.

libtbx_refresh.py

@@ -1,7 +1,10 @@
 import inspect
 import os
+import random
+import site
 import subprocess
 import sys
+from pathlib import Path
 
 import libtbx
 import libtbx.pkg_utils
@@ -19,31 +22,54 @@
     pkg_resources = None
 
 
-def _install_setup_readonly_fallback(package_name: str):
+def _install_dxtbx_setup():
+    """Install xia2 as a regular/editable python package"""
+
+    # We need to find this from libtbx.env because libtbx doesn't read
+    # this properly, as a module - it's just eval'd in scope
+    dxtbx_root_path = libtbx.env.dist_path("dxtbx")
+
+    # Call pip
+    subprocess.run(
+        [
+            sys.executable,
+            "-m",
+            "pip",
+            "install",
+            "--no-build-isolation",
+            "--no-deps",
+            "-e",
+            dxtbx_root_path,
+        ],
+        check=True,
+    )
+
+
+def _install_dxtbx_setup_readonly_fallback():
     """
     Partially install package in the libtbx build folder.
 
     This is a less complete installation - base python console_scripts
     entrypoints will not be installed, but the basic package metadata
     and other entrypoints will be enumerable through dispatcher black magic
     """
-    root_path = libtbx.env.dist_path(package_name)
-    import_path = os.path.join(root_path, "src")
+    dxtbx_root_path = libtbx.env.dist_path("dxtbx")
+    dxtbx_import_path = os.path.join(dxtbx_root_path, "src")
 
     # Install this into a build/dxtbx subfolder
-    build_path = abs(libtbx.env.build_path / package_name)
+    dxtbx_build_path = abs(libtbx.env.build_path / "dxtbx")
     subprocess.run(
         [
             sys.executable,
             "-m",
             "pip",
             "install",
             "--prefix",
-            build_path,
+            dxtbx_build_path,
             "--no-build-isolation",
             "--no-deps",
             "-e",
-            root_path,
+            dxtbx_root_path,
         ],
         check=True,
     )
@@ -54,27 +80,49 @@ def _install_setup_readonly_fallback(package_name: str):
     # Update the libtbx environment pythonpaths to point to the source
     # location which now has an .egg-info folder; this will mean that
     # the PYTHONPATH is written into the libtbx dispatchers
-    rel_path = libtbx.env.as_relocatable_path(import_path)
+    rel_path = libtbx.env.as_relocatable_path(dxtbx_import_path)
     if rel_path not in env.pythonpath:
         env.pythonpath.insert(0, rel_path)
 
     # Update the sys.path so that we can find the .egg-info in this process
     # if we do a full reconstruction of the working set
-    if import_path not in sys.path:
-        sys.path.insert(0, import_path)
+    if dxtbx_import_path not in sys.path:
+        sys.path.insert(0, dxtbx_import_path)
 
     # ...and add to the existing pkg_resources working_set
     if pkg_resources:
-        pkg_resources.working_set.add_entry(import_path)
+        pkg_resources.working_set.add_entry(dxtbx_import_path)
 
     # Also, since we can't re-export dispatchers, add the src/ folder
     # as an extra command_line_locations.
     #
     # This is already generated by this point, but will get picked up
     # on the second libtbx.refresh.
-    module = env.module_dict[package_name]
-    if f"src/{package_name}" not in module.extra_command_line_locations:
-        module.extra_command_line_locations.append(f"src/{package_name}")
+    module = env.module_dict["dxtbx"]
+    if "src/dxtbx" not in module.extra_command_line_locations:
+        module.extra_command_line_locations.append("src/dxtbx")
+
+
+def _test_writable_dir(path: Path) -> bool:
+    """Test a path is writable. Based on pip's _test_writable_dir_win."""
+    # os.access doesn't work on windows
+    # os.access won't always work with network filesystems
+    # pip doesn't use tempfile on windows because https://bugs.python.org/issue22107
+    basename = "test_site_packages_writable_dxtbx_"
+    alphabet = "abcdefghijklmnopqrstuvwxyz0123456789"
+    for _ in range(10):
+        name = basename + "".join(random.choice(alphabet) for _ in range(6))
+        file = path / name
+        try:
+            fd = os.open(file, os.O_RDWR | os.O_CREAT | os.O_EXCL)
+        except FileExistsError:
+            pass
+        except PermissionError:
+            return False
+        else:
+            os.close(fd)
+            os.unlink(file)
+            return True
 
 
 def _get_real_env_hack_hack_hack():
@@ -105,5 +153,18 @@ def _get_real_env_hack_hack_hack():
     raise RuntimeError("Could not determine real libtbx.env_config.environment object")
 
 
-# When building in libtbx, always assume it's unsafe to write to base/
-_install_setup_readonly_fallback("dxtbx")
+# Detect case where base python environment is read-only
+# e.g. on an LCLS session on a custom cctbx installation where the
+# source is editable but the conda_base is read-only
+#
+# We need to check before trying to install as pip does os.access-based
+# checks then installs with --user if it fails. We don't want that.
+# Additionally, if the CCTBX_INSTALL_PACKAGE_BUILD environment variable
+# is set, then we explicitly want to do the readonly fallback.
+if ("CCTBX_INSTALL_PACKAGE_BUILD" not in os.environ) and _test_writable_dir(
+    Path(site.getsitepackages()[0])
+):
+    _install_dxtbx_setup()
+else:
+    print("Python site directory not writable - falling back to tbx install")
+    _install_dxtbx_setup_readonly_fallback()