Merge pull request #11 from NiftyPET/devel

niftypet/ninst/install_tools.py

@@ -77,13 +77,12 @@ def askdir(title, initialdir):
 
 # source and build folder names
 dirsrc = "_src"
-dirbld = Path("_bld")
+dirbld = "_bld"
 
 # number of threads
 ncpu = multiprocessing.cpu_count()
 
 LOG_FORMAT = "%(levelname)s:%(asctime)s:%(name)s:%(funcName)s\n> %(message)s"
-CHUNK_SIZE = 2 ** 15  # 32 kiB
 
 
 class LogHandler(logging.StreamHandler):
@@ -130,36 +129,30 @@ def urlopen_cached(url, outdir, fname=None, mode="rb"):
     fout = outdir / fname
     cache = outdir / f"{fname}.url"
     if not fout.is_file() or not cache.is_file() or cache.read_text().strip() != url:
-        req = request.Request(url=url)
-        with request.urlopen(req) as raw:
-            with tqdm.wrapattr(raw, "read", total=getattr(raw, "length", None)) as fd:
-                with fout.open("wb") as fo:
-                    i = fd.read(CHUNK_SIZE)
-                    while i:
-                        fo.write(i)
-                        i = fd.read(CHUNK_SIZE)
+        fi = request.urlopen(url)
+        with fout.open("wb") as raw:
+            with tqdm.wrapattr(raw, "write", total=getattr(fi, "length", None)) as fo:
+                copyfileobj(fi, fo)
         cache.write_text(url)
     return fout.open(mode)
 
 
 def extractall(fzip, dest, desc="Extracting"):
     """zipfile.Zipfile(fzip).extractall(dest) with progress"""
     dest = Path(dest).expanduser()
-    with ZipFile(fzip) as zipf:
-        with tqdm(
-            desc=desc,
-            unit="B",
-            unit_scale=True,
-            unit_divisor=1024,
-            total=sum(getattr(i, "file_size", 0) for i in zipf.infolist()),
-        ) as pbar:
-            for i in zipf.infolist():
-                if not getattr(i, "file_size", 0):  # directory
-                    zipf.extract(i, fspath(dest))
-                else:
-                    with zipf.open(i) as fi:
-                        with open(fspath(dest / i.filename), "wb") as fo:
-                            copyfileobj(CallbackIOWrapper(pbar.update, fi), fo)
+    with ZipFile(fzip) as zipf, tqdm(
+        desc=desc,
+        unit="B",
+        unit_scale=True,
+        unit_divisor=1024,
+        total=sum(getattr(i, "file_size", 0) for i in zipf.infolist()),
+    ) as pbar:
+        for i in zipf.infolist():
+            if not getattr(i, "file_size", 0):  # directory
+                zipf.extract(i, fspath(dest))
+            else:
+                with zipf.open(i) as fi, open(fspath(dest / i.filename), "wb") as fo:
+                    copyfileobj(CallbackIOWrapper(pbar.update, fi), fo)
 
 
 def query_yesno(question):
@@ -372,9 +365,6 @@ def install_tool(app, Cnt):
     Install the requested software from the git 'repo'
     and check out the version given by 'sha1'.
     """
-    # get the current working directory
-    cwd = os.getcwd()
-
     # pick the target installation folder for tools
     if Cnt.get("PATHTOOLS", None):
         path_tools = Path(Cnt["PATHTOOLS"])
@@ -405,11 +395,11 @@ def install_tool(app, Cnt):
     if app == "niftyreg":
         repo = repo_reg
         sha1 = sha1_reg
-        dest = path_tools / "niftyreg"
+        dest = path_tools.resolve() / "niftyreg"
     elif app == "dcm2niix":
         repo = repo_dcm
         sha1 = sha1_dcm
-        dest = path_tools / "dcm2niix"
+        dest = path_tools.resolve() / "dcm2niix"
 
         if not Cnt["CMPL_DCM2NIIX"]:
             # avoid installing from source, instead download the full version:
@@ -422,40 +412,40 @@ def install_tool(app, Cnt):
     if dest.is_dir():
         rmtree(fspath(dest))
     dest.mkdir()
-    os.chdir(dest)
 
     # clone the git repository
-    run(["git", "clone", repo, dirsrc])
-    os.chdir(dirsrc)
+    run(["git", "clone", repo, fspath(dest / dirsrc)])
     log.info("checking out the specific git version of the software...")
-    run(["git", "checkout", sha1])
-    os.chdir(cwd)
+    run(["git", "-C", fspath(dest / dirsrc), "checkout", sha1])
 
-    dirbld.mkdir(exist_ok=True)
-    os.chdir(dirbld)
+    (dest / dirbld).mkdir(exist_ok=True)
     # run cmake with arguments
     if platform.system() == "Windows":
         run(
             [
                 "cmake",
-                "../" + dirsrc,
+                fspath(dest / dirsrc),
                 "-DBUILD_ALL_DEP=ON",
                 f"-DCMAKE_INSTALL_PREFIX={dest}",
                 "-G",
                 Cnt["MSVC_VRSN"],
-            ]
+            ],
+            cwd=fspath(dest / dirbld),
+        )
+        run(
+            ["cmake", "--build", "./", "--config", "Release", "--target", "install"],
+            cwd=fspath(dest / dirbld),
         )
-        run(["cmake", "--build", "./", "--config", "Release", "--target", "install"])
     elif platform.system() in ["Linux", "Darwin"]:
         cmd = [
             "cmake",
-            "../" + dirsrc,
+            fspath(dest / dirsrc),
             "-DBUILD_ALL_DEP=ON",
             f"-DCMAKE_INSTALL_PREFIX={dest}",
         ]
         if Cnt["CMAKE_TLS_PAR"] != "":
             cmd.append(Cnt["CMAKE_TLS_PAR"])
-        run(cmd)
+        run(cmd, cwd=fspath(dest / dirbld))
         run(
             [
                 "cmake",
@@ -468,12 +458,10 @@ def install_tool(app, Cnt):
                 "--",
                 "-j",
                 str(ncpu),
-            ]
+            ],
+            cwd=fspath(dest / dirbld),
         )
 
-    # restore the current working directory
-    os.chdir(cwd)
-
     if app == "niftyreg":
         try:
             Cnt["RESPATH"] = fspath(next((dest / "bin").glob("reg_resample*")))