Merge pull request #19 from xsuite/release/v0.2.2

Release 0.2.2

make_release_branch.py

@@ -4,8 +4,8 @@
 # Copyright (c) CERN, 2024.                 #
 # ######################################### #
 
-from xaux.tools import dev_make_release_branch
+from xaux.dev_tools import make_release_branch
 # sys.tracebacklimit = 0
 
 
-dev_make_release_branch("xaux")
+make_release_branch("xaux")

pyproject.toml

@@ -1,6 +1,6 @@
 [tool.poetry]
 name = "xaux"
-version = "0.2.1"
+version = "0.2.2"
 description = "Support tools for Xsuite packages"
 authors = ["Frederik F. Van der Veken <[email protected]>",
            "Thomas Pugnat <[email protected]>",
@@ -12,7 +12,7 @@ include = ["LICENSE", "NOTICE"]
 
 
 [tool.poetry.dependencies]
-python = ">=3.8, <3.12"
+python = ">=3.8"
 
 [tool.poetry.dev-dependencies]
 pytest = ">=7.3"

release.py

@@ -4,8 +4,8 @@
 # Copyright (c) CERN, 2024.                 #
 # ######################################### #
 
-from xaux.tools import dev_release
+from xaux.dev_tools import make_release
 # sys.tracebacklimit = 0
 
 
-dev_release("xaux")
+make_release("xaux")

rename_release_branch.py

@@ -4,8 +4,8 @@
 # Copyright (c) CERN, 2024.                 #
 # ######################################### #
 
-from xaux.tools import dev_rename_release_branch
+from xaux.dev_tools import rename_release_branch
 # sys.tracebacklimit = 0
 
 
-dev_rename_release_branch("xaux")
+rename_release_branch("xaux")

tests/clean.sh

@@ -0,0 +1,20 @@
+for f in example_broken_link.txt example_link.txt
+do
+  if [ -h $f ]
+  then
+    rm $f
+  fi
+done
+
+for f in example_file.txt
+do
+  if [ -e $f ]
+  then
+    rm $f
+  fi
+done
+
+rm -r /eos/user/s/sixtadm/test_xboinc/*
+rm -r /afs/cern.ch/user/s/sixtadm/public/test_xboinc
+rm -r level1 level5_res
+

tests/conftest.py

@@ -49,4 +49,4 @@ def test_user(request):
                             + "your access rights (is your ticket still alive?).\nAlternatively, specify the test "
                             + "user account with the option `--user username`\nI Tried the following paths:\n    "
                             + "\n    ".join(eos_paths_tried) + "\nThe relevant EosPath tests will be skipped.")
-    return {"test_user": test_user, "afs_path":  afs_path, "skip_afs": skip_afs, "eos_path":  eos_path, "skip_eos": skip_eos}
+    return {"test_user": test_user, "afs_path": afs_path, "skip_afs": skip_afs, "eos_path": eos_path, "skip_eos": skip_eos}

tests/pytest_all_versions.sh

@@ -3,7 +3,7 @@
 # files="test_fs.py test_fs_api.py test_fs_afs.py test_fs_eos.py"
 files=''
 
-for i in 8 9 10 11 # 12 13
+for i in 8 9 10 11 12 13
 do
     source ~/miniforge3/bin/activate python3.$i
     python -c "import sys; print(f'Testing xaux FS in Python version {sys.version.split()[0]}')"

tests/test_fs.py

@@ -192,15 +192,41 @@ def test_nested_fs(test_user):
         level6.unlink()
     level6.symlink_to(level6_res)
 
+    for l in [level1, level2, level3, level4, level5, level6]:
+        assert l.lexists()
+        assert l.is_symlink()
+    for d in [level1_res, level2_res, level3_res, level4_res, level5_res, level6_res]:
+        assert d.exists()
+        assert d.is_dir()
+        assert not d.is_symlink()
+    for l, d in zip([level1, level2, level3, level4, level5, level6],
+                    [level1_res, level2_res, level3_res, level4_res, level5_res, level6_res]):
+        assert l.resolve() == d
+
+    assert isinstance(level1, AfsPath)
+    assert isinstance(level2, LocalPath)
+    assert isinstance(level3, EosPath)
+    assert isinstance(level4, AfsPath)
+    assert isinstance(level5, EosPath)
+    assert isinstance(level6, LocalPath)
+    assert isinstance(level1_res, LocalPath)
+    assert isinstance(level2_res, EosPath)
+    assert isinstance(level3_res, AfsPath)
+    assert isinstance(level4_res, EosPath)
+    assert isinstance(level5_res, LocalPath)
+    assert isinstance(level6_res, AfsPath)
+
     path = level1 / "level2" / "level3" / "level4" / "level5" / "level6"
     assert isinstance(path, LocalPath)
     parents = [f for f in path.parents]
+    assert len(parents) == 13
     expected = [EosPath, AfsPath, EosPath, LocalPath, AfsPath,
                 AfsPath, AfsPath, AfsPath, AfsPath, AfsPath,
                 AfsPath, LocalPath, LocalPath]
     assert all([isinstance(f, exp) for f, exp in zip(parents, expected)])
     assert isinstance(path.resolve(), AfsPath)
     parents_res = [f.resolve() for f in path.parents]
+    assert len(parents_res) == 13
     expected_res = [LocalPath, EosPath, AfsPath, EosPath, LocalPath,
                     AfsPath, AfsPath, AfsPath, AfsPath, AfsPath,
                     AfsPath, LocalPath, LocalPath]

tests/test_fs_eos.py

@@ -255,8 +255,8 @@ def test_eos_components(test_user):
     broken_mgm_files.append(f"root:/eoshome.cern.ch/{file_ref}")
     broken_mgm_files.append(f"root://afshome.cern.ch/{file_ref}")
     for file in broken_mgm_files:
-        with pytest.raises(ValueError, match="Invalid EOS path specification"):
+        with pytest.raises(ValueError, match="Invalid EosPath specification"):
             path = EosPath(file)
-    with pytest.raises(ValueError, match="Unknown path specification"):
+    with pytest.raises(ValueError, match="Unknown EosPath specification"):
         path = FsPath(broken_mgm_files[-1])
 

tests/test_version.py

@@ -6,5 +6,5 @@
 from xaux import __version__
 
 def test_version():
-    assert __version__ == '0.2.1'
+    assert __version__ == '0.2.2'
 

xaux/__init__.py

@@ -3,10 +3,7 @@
 # Copyright (c) CERN, 2024.                 #
 # ######################################### #
 
-import sys
-if sys.version_info[1] >= 12:
-    raise Exception("Must be using Python 3.8 - 3.11")
-
 from .general import _pkg_root, __version__
 from .protectfile import ProtectFile, ProtectFileError, get_hash
 from .fs import FsPath, LocalPath, EosPath, AfsPath, afs_accessible, eos_accessible, is_egroup_member, cp, mv
+from .dev_tools import import_package_version  # Stub

xaux/dev_tools/__init__.py

@@ -0,0 +1,7 @@
+# copyright ############################### #
+# This file is part of the Xaux Package.    #
+# Copyright (c) CERN, 2024.                 #
+# ######################################### #
+
+from .release_tools import make_release, make_release_branch, rename_release_branch
+from .package_manager import *

xaux/tools/gh.py → xaux/dev_tools/gh.py

@@ -1,7 +1,7 @@
 import sys
 import json
 from pathlib import Path
-from subprocess import run, PIPE
+from subprocess import run
 
 _GIT_REPO = False
 _GH_INSTALLED = False
@@ -11,37 +11,49 @@
 def assert_git_repo():
     global _GIT_REPO
     if not _GIT_REPO:
-        cmd = run(["git", "status"], capture_output=True)
+        try:
+            cmd = run(["git", "status"], capture_output=True)
+            if cmd.returncode != 0:
+                raise GitError(f"{Path.cwd()} is not a git repository.")
+            else:
+                _GIT_REPO = True
+        except FileNotFoundError:
+            raise GitError("git is not installed.")
+
+def assert_git_repo_name(repo):
+    try:
+        cmd = run(["git", "rev-parse", "--show-toplevel"], capture_output=True)
         if cmd.returncode != 0:
             raise GitError(f"{Path.cwd()} is not a git repository.")
         else:
-            _GIT_REPO = True
-
-def assert_git_repo_name(repo):
-    cmd = run(["git", "rev-parse", "--show-toplevel"], capture_output=True)
-    if cmd.returncode != 0:
-        raise GitError(f"{Path.cwd()} is not a git repository.")
-    else:
-        if Path(cmd.stdout.decode('UTF-8').strip()).name != repo:
-            raise GitError(f"{Path.cwd()} is not in the {repo} repository.")
+            if Path(cmd.stdout.decode('UTF-8').strip()).name != repo:
+                raise GitError(f"{Path.cwd()} is not in the {repo} repository.")
+    except FileNotFoundError:
+        raise GitError("git is not installed.")
 
 def assert_gh_installed():
     global _GH_INSTALLED
     if not _GH_INSTALLED:
-        cmd = run(["gh", "--version"], capture_output=True)
-        if cmd.returncode != 0:
+        try:
+            cmd = run(["gh", "--version"], capture_output=True)
+            if cmd.returncode != 0:
+                raise GhError("gh is not installed.")
+            else:
+                _GH_INSTALLED = True
+        except FileNotFoundError:
             raise GhError("gh is not installed.")
-        else:
-            _GH_INSTALLED = True
 
 def assert_poetry_installed():
     global _POETRY_INSTALLED
     if not _POETRY_INSTALLED:
-        cmd = run(["poetry", "--version"], capture_output=True)
-        if cmd.returncode != 0:
+        try:
+            cmd = run(["poetry", "--version"], capture_output=True)
+            if cmd.returncode != 0:
+                raise PoetryError("poetry is not installed.")
+            else:
+                _POETRY_INSTALLED = True
+        except FileNotFoundError:
             raise PoetryError("poetry is not installed.")
-        else:
-            _POETRY_INSTALLED = True
 
 
 def git_assert_working_tree_clean():

xaux/dev_tools/package_manager.py

@@ -0,0 +1,151 @@
+# copyright ############################### #
+# This file is part of the Xaux Package.    #
+# Copyright (c) CERN, 2024.                 #
+# ######################################### #
+
+import os
+import sys
+import json
+import importlib
+import urllib.request
+from shutil import rmtree
+from subprocess import run
+from contextlib import contextmanager
+from packaging.version import Version
+
+from ..general import _pkg_root
+
+
+_PACKAGE_PATH = _pkg_root / "lib" / "_xaux_pkg_vers"
+
+xsuite_pkgs = ['xaux', 'xobjects', 'xdeps', 'xtrack', 'xpart', 'xfields', 'xcoll', 'xdyna', 'xboinc']
+
+
+@contextmanager
+def import_package_version(package_name, version, wipe_cache=False):
+    """
+    Context manager to temporarily import a specific version of a package.
+    """
+    package_path = _PACKAGE_PATH / package_name / version
+    if not package_path.exists():
+        install_package_version(package_name, version)
+
+    original_sys_path = sys.path.copy()
+    original_sys_modules = sys.modules.copy()
+    original_sys_meta_path = sys.meta_path.copy()
+    pkgs = _get_available_packages_in_path(package_path)
+    for pkg in pkgs:
+        _remove_import_from_sys(pkg)
+    for finder_name in sys.meta_path:
+        if package_name in str(finder_name):
+            sys.meta_path.remove(finder_name)
+    if wipe_cache:
+        importlib.invalidate_caches()
+        for finder_name in sys.meta_path:
+            if 'editable' in str(finder_name):
+                sys.meta_path.remove(finder_name)
+    sys.path.insert(0, package_path.as_posix())
+    try:
+        module = importlib.import_module(package_name)
+        yield module
+    finally:
+        sys.path = original_sys_path
+        sys.modules = original_sys_modules
+        sys.meta_path = original_sys_meta_path
+
+
+def install_package_version(package_name, version, overwrite=False):
+    """
+    Installs a specific version of a package.
+    """
+    full_package_name = f"{package_name}=={version}"
+    package_path = _PACKAGE_PATH / package_name / version
+    if package_path.exists() and not overwrite:
+        print(f"Package already installed in {package_path}. "
+             + "Use `overwrite=True` if this is the intended goal.")
+    else:
+        if package_path.exists():
+            rmtree(package_path)
+        package_path.mkdir(parents=True)
+        try:
+            print(f"Installing package {full_package_name}")
+            cmd = run([sys.executable, "-m", "pip", "install", full_package_name,
+                    f"--target={package_path}"], capture_output=True)
+            if cmd.returncode != 0:
+                print(f"Installation failed for {full_package_name}:\n{cmd.stderr.decode()}")
+        except Exception as e:
+            print(f"An error occurred: {e}\nCommand output:{cmd.stderr.decode()}")
+
+
+def get_package_versions(package_name):
+    """
+    Get all available versions of a package from PyPI, sorted by newest last.
+    """
+    data = json.loads(urllib.request.urlopen(f"https://pypi.org/pypi/{package_name}/json").read())
+    return sorted(list(data['releases'].keys()), key=Version)
+
+
+def get_latest_package_version(package_name):
+    """
+    Get the latest version of a package from PyPI.
+    """
+    data = json.loads(urllib.request.urlopen(f"https://pypi.org/pypi/{package_name}/json").read())
+    return data['info']['version']
+
+
+def get_package_dependencies(package_name):
+    """
+    Get the dependencies of a package from PyPI.
+    """
+    data = json.loads(urllib.request.urlopen(f"https://pypi.org/pypi/{package_name}/json").read())
+    return data['info']['requires_dist']
+
+
+def get_package_version_dependencies(package_name, version, skip=[]):
+    """
+    Get the package versions of the dependencies for a specific version of `package_name`.
+    TODO: This function is not working as intended when `numpy` is a dependency and already imported.
+    """
+    if not hasattr(skip, '__iter__') or isinstance(skip, str):
+        skip = [skip]
+    deps = {}
+    with import_package_version(package_name, version, wipe_cache=True):
+        package_path = _PACKAGE_PATH / package_name / version
+        pkgs = _get_available_packages_in_path(package_path)
+        pkgs = [pkg for pkg in pkgs if pkg not in skip]
+        # for pkg in pkgs:
+        #     _remove_import_from_sys(pkg)
+        for pkg in pkgs:
+            if pkg in ['numpy', 'numba', 'scipy']:
+                # These are being difficult
+                deps[pkg] = None
+            else:
+                # mod = _import_package_from_path(pkg, package_path)
+                mod = importlib.import_module(pkg)
+                assert mod.__file__.startswith(package_path.as_posix())
+                deps[pkg] = mod.__version__ if hasattr(mod, '__version__') else None
+    return deps
+
+
+def _get_available_packages_in_path(path):
+    return [pkg.name for pkg in path.glob('*') if (path / pkg).is_dir() \
+            and not pkg.name.startswith('_') and not '.' in pkg.name \
+            and not pkg.name.endswith('dist-info') and not pkg.name == 'bin']
+
+
+def _remove_import_from_sys(package_name):
+    for mod_name in list(sys.modules):
+        if package_name == mod_name or mod_name.startswith(package_name + '.'):
+            del sys.modules[mod_name]
+
+def _import_package_from_path(package_name, package_path):
+    original_sys_path = sys.path.copy()
+    original_sys_meta_path = sys.meta_path.copy()
+    for finder_name in sys.meta_path:
+        if package_name in str(finder_name):
+            sys.meta_path.remove(finder_name)
+    sys.path.insert(0, package_path.as_posix())
+    module = importlib.import_module(package_name)
+    sys.path = original_sys_path
+    sys.meta_path = original_sys_meta_path
+    return module