easyxrd 0.1.3__py3-none-any.whl

easyxrd/__init__.py

@@ -0,0 +1,245 @@
+import sys
+import os
+import subprocess
+
+import importlib
+from importlib.metadata import version
+
+import shutil
+import numpy as np
+import urllib.request
+
+import tarfile
+import time
+
+import platform
+
+
+class HiddenPrints:
+    """
+    This class hides print outputs from functions. It is useful for processes like refinement which produce a lot of text prints.
+    """
+
+    def __enter__(self):
+        self._original_stdout = sys.stdout
+        sys.stdout = open(os.devnull, "w")
+
+    def __exit__(self, exc_type, exc_val, exc_tb):
+        sys.stdout.close()
+        sys.stdout = self._original_stdout
+
+
+print("\n\nPython=%d.%d.%d | Platform=%s"%(sys.version_info.major,sys.version_info.minor,sys.version_info.micro,platform.platform()))
+print("Checking required packages:\n")
+# These are big python libraries that we will need in pySULI.
+# If the required library doesn't exist, we can it via pip
+
+required_packages = {
+    "numpy",
+    "scipy",
+    "xarray",
+    "ipympl",
+    "pymatgen",
+    "pyFAI",
+    "fabio",
+    "pybaselines",
+    "mp_api",
+}
+
+failed_packages = []
+for rp in required_packages:
+    try:
+        globals()[rp] = importlib.import_module(rp)
+        print(
+            "---%s package with version %s is available and can be imported "
+            % (rp, version(rp))
+        )
+    except:
+        failed_packages.append(rp)
+
+
+for fp in failed_packages:
+    print("\n\n----Failed to import %s" % fp)
+    print('Try installing it via `pip install %s`\n'% fp.replace('_','-'))
+
+
+
+# defaults
+easyxrd_defaults = dict()
+user_home = os.path.expanduser("~")
+
+
+# Setting up easyxrd_scratch folder
+if not os.path.isdir(os.path.join(user_home, ".easyxrd_scratch")):
+    os.mkdir(os.path.join(user_home, ".easyxrd_scratch"))
+easyxrd_defaults["easyxrd_scratch_path"] = os.path.join(user_home, ".easyxrd_scratch")
+
+
+# Get GSAS-II and binaries from GitHub
+
+gsas2_path_in_easyxrd_scratch = os.path.join(user_home, ".easyxrd_scratch", "GSAS-II")
+sys.path += [os.path.join(gsas2_path_in_easyxrd_scratch, "GSASII")]
+
+try:
+    with HiddenPrints():
+        import GSASIIscriptable as G2sc
+        print(
+            "\nFound usable GSAS-II lib path @ %s"
+            % os.path.join(gsas2_path_in_easyxrd_scratch, "GSASII")
+        )
+    easyxrd_defaults["gsasii_lib_path"] = os.path.join(
+        gsas2_path_in_easyxrd_scratch, "GSASII"
+    )
+except Exception as exc:
+    # print(exc)
+    if os.path.isdir(gsas2_path_in_easyxrd_scratch):
+        shutil.rmtree(gsas2_path_in_easyxrd_scratch)
+
+    # print("\nClonning GSAS-II package from GitHub")
+    # import git
+    # git.Repo.clone_from(
+    #     "https://github.com/AdvancedPhotonSource/GSAS-II",
+    #     to_path=gsas2_path_in_easyxrd_scratch,
+    #     multi_options=["--depth 1"],
+    # )
+
+    print("\nDownloading GSAS-II (version 5805) from GitHub")
+    urllib.request.urlretrieve(
+        "https://github.com/AdvancedPhotonSource/GSAS-II/archive/refs/tags/5805.tar.gz",
+        os.path.join(easyxrd_defaults["easyxrd_scratch_path"], "GSAS-5805.tar.gz"),
+    ),
+
+    with tarfile.open(
+        os.path.join(easyxrd_defaults["easyxrd_scratch_path"], "GSAS-5805.tar.gz"),
+        "r:gz",
+    ) as tar:
+        tar.extractall(os.path.join(easyxrd_defaults["easyxrd_scratch_path"]))
+    os.rename(
+        os.path.join(easyxrd_defaults["easyxrd_scratch_path"], "GSAS-II-5805"),
+        os.path.join(easyxrd_defaults["easyxrd_scratch_path"], "GSAS-II"),
+    )
+
+
+    try:
+        gsas_file_to_fix = os.path.join(easyxrd_defaults["easyxrd_scratch_path"], "GSAS-II", "GSASII", "NIST_profile", "profile_functions_class.py")
+
+        if os.path.isfile(gsas_file_to_fix):
+            with open(gsas_file_to_fix, 'r') as pfile:
+                pcontent = pfile.read()
+            modified_pcontent = pcontent.replace("xrange", "range")
+            with open(gsas_file_to_fix, 'w') as pmfile:
+                pmfile.write(modified_pcontent)
+
+    except:
+        pass
+            
+
+
+
+    os.makedirs(
+        os.path.join(gsas2_path_in_easyxrd_scratch, "GSASII-bin"), exist_ok=True
+    )
+
+    if (platform.system() == "Linux") and (platform.machine() == 'x86_64'):
+        os_str = "linux_64"
+    elif (platform.system() == "Windows") and (platform.machine() == 'AMD64'):
+        os_str = "win_64"
+    elif (platform.system() == "Darvin") and (platform.machine() == 'x86_64'):
+        os_str = "mac_64"
+    else:
+        os_str = "mac_arm"
+
+
+    py_str = "p%d.%d" % (sys.version_info.major, sys.version_info.minor)
+    np_str = "n%s.%s" % (
+        np.version.version.split(".")[0],
+        np.version.version.split(".")[1],
+    )
+    gsas2_bin_tgz = (
+        "https://github.com/AdvancedPhotonSource/GSAS-II-buildtools/releases/download/v1.0.1/%s_%s_%s.tgz"
+        % (os_str, py_str, np_str)
+    )
+    print(gsas2_bin_tgz)
+
+    os.makedirs(
+        os.path.join(
+            gsas2_path_in_easyxrd_scratch,
+            "GSASII-bin",
+            gsas2_bin_tgz.split("/")[-1][:-4],
+        ),
+        exist_ok=True,
+    )
+
+    try:
+        print("Downloading %s from GitHub" % gsas2_bin_tgz)
+        urllib.request.urlretrieve(
+            gsas2_bin_tgz,
+            os.path.join(
+                gsas2_path_in_easyxrd_scratch,
+                "GSASII-bin",
+                gsas2_bin_tgz.split("/")[-1][:-4],
+                "bin.tgz",
+            ),
+        )
+        with tarfile.open(
+            os.path.join(
+                gsas2_path_in_easyxrd_scratch,
+                "GSASII-bin",
+                gsas2_bin_tgz.split("/")[-1][:-4],
+                "bin.tgz",
+            ),
+            "r:gz",
+        ) as tar:
+            tar.extractall(
+                path=os.path.join(
+                    gsas2_path_in_easyxrd_scratch,
+                    "GSASII-bin",
+                    gsas2_bin_tgz.split("/")[-1][:-4],
+                )
+            )
+        easyxrd_defaults["gsasii_lib_path"] = os.path.join(
+            gsas2_path_in_easyxrd_scratch, "GSASII"
+        )
+
+        print(
+            "\n!!!! Please re-run this cell (after kernel restart) for the GSAS-II installation to take effect !!!!!"
+        )
+        time.sleep(2)
+        os._exit(1)
+    except Exception as exc:
+        print(exc)
+        easyxrd_defaults["gsasii_lib_path"] = "not found"
+
+
+# check Materials Project API key in easyxrd_scratch folder
+if os.path.isfile(os.path.join(user_home, ".easyxrd_scratch", "mp_api_key.dat")):
+    with open(
+        os.path.join(user_home, ".easyxrd_scratch", "mp_api_key.dat"), "r"
+    ) as api_key_file:
+        api_key_file_content = api_key_file.read().split()[-1]
+        if len(api_key_file_content) == 32:
+            mp_api_key = api_key_file_content
+        else:
+            mp_api_key = "invalid"
+else:
+    mp_api_key = "not found"
+easyxrd_defaults["mp_api_key"] = mp_api_key
+
+
+def set_defaults(name, val):
+    """set a global variable."""
+    global easyxrd_defaults
+    easyxrd_defaults[name] = val
+
+
+def print_defaults():
+    for key, val in easyxrd_defaults.items():
+
+        if key != "mp_api_key":
+            print("%s : %s" % (key, val))
+        else:
+            print("%s : %s.........." % (key, val[:9]))
+
+
+print("\n\nImported easyxrd with the following configuration:\n")
+print_defaults()