pdal: new package (#42714)

* new package pdal

* [@spackbot] updating style on behalf of Sinan81

* fix style

* add license

* Update var/spack/repos/builtin/packages/pdal/package.py

Co-authored-by: Alec Scott <alec@bcs.sh>

* [@spackbot] updating style on behalf of Sinan81

* Update var/spack/repos/builtin/packages/pdal/package.py

Co-authored-by: Alec Scott <alec@bcs.sh>

* Update var/spack/repos/builtin/packages/pdal/package.py

Co-authored-by: Alec Scott <alec@bcs.sh>

* improve dependency spec

* add maintainer

* add conflict

* fix bug

* improve

* improve

* [@spackbot] updating style on behalf of Sinan81

* fix style

* specify cmake dependency version

---------

Co-authored-by: sbulut <sbulut@3vgeomatics.com>
Co-authored-by: Sinan81 <Sinan81@users.noreply.github.com>
Co-authored-by: Alec Scott <alec@bcs.sh>

lib/spack/spack/cmd/common/env_utility.py

@@ -115,7 +115,7 @@ def emulate_env_utility(cmd_name, context: Context, args):
             f"Not all dependencies of {spec.name} are installed. "
             f"Cannot setup {context} environment:",
             spec.tree(
-                install_status=True,
+                status_fn=spack.spec.Spec.install_status,
                 hashlen=7,
                 hashes=True,
                 # This shows more than necessary, but we cannot dynamically change deptypes

lib/spack/spack/cmd/solve.py

@@ -135,6 +135,8 @@ def _process_result(result, show, required_format, kwargs):
 
 def solve(parser, args):
     # these are the same options as `spack spec`
+    install_status_fn = spack.spec.Spec.install_status
+
     fmt = spack.spec.DISPLAY_FORMAT
     if args.namespaces:
         fmt = "{namespace}." + fmt
@@ -144,7 +146,7 @@ def solve(parser, args):
         "format": fmt,
         "hashlen": None if args.very_long else 7,
         "show_types": args.types,
-        "install_status": args.install_status,
+        "status_fn": install_status_fn if args.install_status else None,
         "hashes": args.long or args.very_long,
     }
 

lib/spack/spack/cmd/spec.py

@@ -75,6 +75,8 @@ def setup_parser(subparser):
 
 
 def spec(parser, args):
+    install_status_fn = spack.spec.Spec.install_status
+
     fmt = spack.spec.DISPLAY_FORMAT
     if args.namespaces:
         fmt = "{namespace}." + fmt
@@ -84,7 +86,7 @@ def spec(parser, args):
         "format": fmt,
         "hashlen": None if args.very_long else 7,
         "show_types": args.types,
-        "install_status": args.install_status,
+        "status_fn": install_status_fn if args.install_status else None,
     }
 
     # use a read transaction if we are getting install status for every

lib/spack/spack/environment/environment.py

@@ -2212,7 +2212,7 @@ def _tree_to_display(spec):
         return spec.tree(
             recurse_dependencies=True,
             format=spack.spec.DISPLAY_FORMAT,
-            install_status=True,
+            status_fn=spack.spec.Spec.install_status,
             hashlen=7,
             hashes=True,
         )

lib/spack/spack/spec.py

@@ -186,11 +186,11 @@ class InstallStatus(enum.Enum):
     Options are artificially disjoint for display purposes
     """
 
-    INSTALLED = "@g{[+]}"
-    UPSTREAM = "@g{[^]}"
-    EXTERNAL = "@g{[e]}"
-    ABSENT = "@K{ - }"
-    MISSING = "@r{[-]}"
+    installed = "@g{[+]}  "
+    upstream = "@g{[^]}  "
+    external = "@g{[e]}  "
+    absent = "@K{ - }  "
+    missing = "@r{[-]}  "
 
 
 def colorize_spec(spec):
@@ -1499,7 +1499,7 @@ def edge_attributes(self) -> str:
         if not deptypes_str and not virtuals_str:
             return ""
         result = f"{deptypes_str} {virtuals_str}".strip()
-        return f"[{result}] "
+        return f"[{result}]"
 
     def dependencies(
         self, name=None, deptype: Union[dt.DepTypes, dt.DepFlag] = dt.ALL
@@ -4319,7 +4319,8 @@ def colorized(self):
         return colorize_spec(self)
 
     def format(self, format_string=DEFAULT_FORMAT, **kwargs):
-        r"""Prints out particular pieces of a spec, depending on what is in the format string.
+        r"""Prints out particular pieces of a spec, depending on what is
+        in the format string.
 
         Using the ``{attribute}`` syntax, any field of the spec can be
         selected.  Those attributes can be recursive. For example,
@@ -4445,9 +4446,6 @@ def write_attribute(spec, attribute, color):
             elif attribute == "spack_install":
                 write(morph(spec, spack.store.STORE.layout.root))
                 return
-            elif re.match(r"install_status", attribute):
-                write(self.install_status_symbol())
-                return
             elif re.match(r"hash(:\d)?", attribute):
                 col = "#"
                 if ":" in attribute:
@@ -4542,18 +4540,8 @@ def write_attribute(spec, attribute, color):
                 "Format string terminated while reading attribute." "Missing terminating }."
             )
 
-        # remove leading whitespace from directives that add it for internal formatting.
-        # Arch, compiler flags, and variants add spaces for spec format correctness, but
-        # we don't really want them in formatted string output. We do want to preserve
-        # whitespace from the format string.
         formatted_spec = out.getvalue()
-        whitespace_attrs = [r"{arch=[^}]*}", r"{architecture}", r"{compiler_flags}", r"{variants}"]
-        if any(re.match(rx, format_string) for rx in whitespace_attrs):
-            formatted_spec = formatted_spec.lstrip()
-        if any(re.search(f"{rx}$", format_string) for rx in whitespace_attrs):
-            formatted_spec = formatted_spec.rstrip()
-
-        return formatted_spec
+        return formatted_spec.strip()
 
     def cformat(self, *args, **kwargs):
         """Same as format, but color defaults to auto instead of False."""
@@ -4603,7 +4591,7 @@ def __str__(self):
             self.traverse(root=False), key=lambda x: (x.name, x.abstract_hash)
         )
         sorted_dependencies = [
-            d.format("{edge_attributes}" + DEFAULT_FORMAT) for d in sorted_dependencies
+            d.format("{edge_attributes} " + DEFAULT_FORMAT) for d in sorted_dependencies
         ]
         spec_str = " ^".join(root_str + sorted_dependencies)
         return spec_str.strip()
@@ -4623,25 +4611,20 @@ def colored_str(self):
     def install_status(self):
         """Helper for tree to print DB install status."""
         if not self.concrete:
-            return InstallStatus.ABSENT
+            return InstallStatus.absent
 
         if self.external:
-            return InstallStatus.EXTERNAL
+            return InstallStatus.external
 
         upstream, record = spack.store.STORE.db.query_by_spec_hash(self.dag_hash())
         if not record:
-            return InstallStatus.ABSENT
+            return InstallStatus.absent
         elif upstream and record.installed:
-            return InstallStatus.UPSTREAM
+            return InstallStatus.upstream
         elif record.installed:
-            return InstallStatus.INSTALLED
+            return InstallStatus.installed
         else:
-            return InstallStatus.MISSING
-
-    def install_status_symbol(self):
-        """Get an install status symbol."""
-        status = self.install_status()
-        return clr.colorize(status.value)
+            return InstallStatus.missing
 
     def _installed_explicitly(self):
         """Helper for tree to print DB install status."""
@@ -4667,7 +4650,7 @@ def tree(
         show_types: bool = False,
         depth_first: bool = False,
         recurse_dependencies: bool = True,
-        install_status: bool = False,
+        status_fn: Optional[Callable[["Spec"], InstallStatus]] = None,
         prefix: Optional[Callable[["Spec"], str]] = None,
     ) -> str:
         """Prints out this spec and its dependencies, tree-formatted
@@ -4688,7 +4671,8 @@ def tree(
             show_types: if True, show the (merged) dependency type of a node
             depth_first: if True, traverse the DAG depth first when representing it as a tree
             recurse_dependencies: if True, recurse on dependencies
-            install_status: if True, show installation status next to each spec
+            status_fn: optional callable that takes a node as an argument and return its
+                installation status
             prefix: optional callable that takes a node as an argument and return its
                 installation prefix
         """
@@ -4702,9 +4686,6 @@ def tree(
         ):
             node = dep_spec.spec
 
-            if install_status:
-                out += node.format("{install_status}  ")
-
             if prefix is not None:
                 out += prefix(node)
             out += " " * indent
@@ -4712,6 +4693,15 @@ def tree(
             if depth:
                 out += "%-4d" % d
 
+            if status_fn:
+                status = status_fn(node)
+                if status in list(InstallStatus):
+                    out += clr.colorize(status.value, color=color)
+                elif status:
+                    out += clr.colorize("@g{[+]}  ", color=color)
+                else:
+                    out += clr.colorize("@r{[-]}  ", color=color)
+
             if hashes:
                 out += clr.colorize("@K{%s}  ", color=color) % node.dag_hash(hashlen)
 

lib/spack/spack/test/spec_semantics.py

@@ -703,13 +703,6 @@ def check_prop(check_spec, fmt_str, prop, getter):
             actual = spec.format(named_str)
             assert expected == actual
 
-    def test_spec_format_instalL_status(self, database):
-        installed = database.query_one("mpileaks^zmpi")
-        assert installed.format("{install_status}") == "[+]"
-
-        not_installed = Spec("foo")
-        assert not_installed.format("{install_status}") == " - "
-
     def test_spec_formatting_escapes(self, default_mock_concretization):
         spec = default_mock_concretization("multivalue-variant cflags=-O2")
 

var/spack/repos/builtin/packages/cryodrgn/package.py

@@ -0,0 +1,38 @@
+# Copyright 2013-2024 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack.package import *
+
+
+class Cryodrgn(PythonPackage):
+    """CryoDRGN is a neural network based algorithm for heterogeneous cryo-EM reconstruction.
+    In particular, the method models a continuous distribution over 3D structures by using a
+    neural network based representation for the volume"""
+
+    homepage = "https://cryodrgn.cs.princeton.edu/"
+    pypi = "cryodrgn/cryodrgn-2.3.0.tar.gz"
+
+    license("GPL-3.0-only", checked_by="A-N-Other")
+
+    version("2.3.0", sha256="9dd75967fddfa56d6b2fbfc56933c50c9fb994326112513f223e8296adbf0afc")
+
+    depends_on("python@3.7:", type=("build", "run"))
+
+    depends_on("py-setuptools@61:", type="build")
+    depends_on("py-setuptools-scm@6.2:", type="build")
+
+    depends_on("py-torch@1:", type=("build", "run"))
+    depends_on("py-pandas@:1", type=("build", "run"))
+    depends_on("py-numpy", type=("build", "run"))
+    depends_on("py-matplotlib", type=("build", "run"))
+    depends_on("py-pyyaml", type=("build", "run"))
+    depends_on("py-scipy@1.3.1:", type=("build", "run"))
+    depends_on("py-scikit-learn", type=("build", "run"))
+    depends_on("py-seaborn@:0.11", type=("build", "run"))
+    depends_on("py-cufflinks", type=("build", "run"))
+    depends_on("py-jupyterlab", type=("build", "run"))
+    depends_on("py-umap-learn", type=("build", "run"))
+    depends_on("py-ipywidgets@:7", type=("build", "run"))
+    depends_on("py-healpy", type=("build", "run"))

var/spack/repos/builtin/packages/pdal/package.py

@@ -0,0 +1,42 @@
+# Copyright 2013-2023 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack.package import *
+
+
+class Pdal(CMakePackage):
+    """PDAL is a C++ library for translating and manipulating point cloud data.
+    It is very much like the GDAL library which handles raster and vector data.
+    """
+
+    homepage = "https://pdal.io"
+    url = "https://github.com/PDAL/PDAL/archive/refs/tags/2.6.2.tar.gz"
+
+    maintainers("adamjstewart")
+
+    license("BSD")
+
+    version("2.6.2", sha256="ec4175cfe19dc6b70a0434850f837317f7202f84b63cd8dcc65ca83e04678f57")
+    version("2.6.1", sha256="da6e615f01b6110414ef3e2250f112e49df129091abc91ba6866bb01dc68454e")
+    version("2.6.0", sha256="12eedeac16ec3aaef42f06078f03f657701c25781207a8e09a3547519228780e")
+    version("2.5.6", sha256="de4177305e380d21187da8ec90afda64756bbde5e925035bd53e54a6e349df18")
+    version("2.5.5", sha256="6bf4f34bc0bf1bce52b8daecb03a7f45d218c0374bfa00783c787b9e54d56d72")
+    version("2.4.3", sha256="e1a910d593311e68b51f32d1f4f8fe4327b97ae7a8de209147b6111091b6f75b")
+    version("2.3.0", sha256="8ae848e9b3fe5149a9277fe60e10b9858edb9a3cf1a40728f11712498e5da13a")
+
+    depends_on("cmake@3.13:", type="build")
+    depends_on("gdal@3:")
+    depends_on("gdal@3.4:", when="@2.6:")
+    depends_on("gdal@:3.6", when="@:2.4")
+    depends_on("libgeotiff@1.3.0:")
+    depends_on("proj@4.9.3:")
+
+    # https://github.com/PDAL/PDAL/issues/3826
+    patch("stdcppfs.patch", when="@:2.6.1 %gcc@:8")
+    msg = "a new stdc++fs patch is needed for version 2.6.2 onwards with gcc@8 or older"
+    conflicts("%gcc@:8", when="@2.6.2:", msg=msg)
+
+    def cmake_args(self):
+        return [self.define("PROJ_INCLUDE_DIR", self.spec["proj"].prefix.include)]

var/spack/repos/builtin/packages/pdal/stdcppfs.patch

@@ -0,0 +1,8 @@
+--- spack-src/pdal/util/CMakeLists.txt	2022-08-05 10:29:13.000000000 -0700
++++ spack-src/pdal/util/CMakeLists.txt_new	2024-02-15 17:50:10.882186258 -0800
+@@ -46,3 +46,5 @@
+     CLEAN_DIRECT_OUTPUT 1)
+ 
+ set_property(GLOBAL PROPERTY _UTIL_INCLUDED TRUE)
++
++target_link_libraries(${PDAL_UTIL_LIB_NAME} PRIVATE -lstdc++fs)

var/spack/repos/builtin/packages/py-azure-batch/package.py

@@ -13,9 +13,20 @@ class PyAzureBatch(PythonPackage):
     homepage = "https://github.com/Azure/azure-sdk-for-python"
     pypi = "azure-batch/azure-batch-9.0.0.zip"
 
+    version("14.0.0", sha256="165b1e99b86f821024c4fae85fb34869d407aa0ebb0ca4b96fb26d859c26c934")
+    version("13.0.0", sha256="e9295de70404d276eda0dd2253d76397439abe5d8f18c1fca199c49b8d6ae30a")
+    version("12.0.0", sha256="1a9b1e178984a7bf495af67bcce51f0db1e4a8a957afb29e33554a14a9674deb")
+    version("11.0.0", sha256="ce5fdb0ec962eddfe85cd82205e9177cb0bbdb445265746e38b3bbbf1f16dc73")
+    version("10.0.0", sha256="83d7a2b0be42ca456ac2b56fa3dc6ce704c130e888d37d924072c1d3718f32d0")
     version("9.0.0", sha256="47ca6f50a640915e1cdc5ce3c1307abe5fa3a636236e561119cf62d9df384d84")
 
+    # https://github.com/Azure/azure-sdk-for-python/blob/azure-batch_14.0.0/sdk/batch/azure-batch/setup.py
+
     depends_on("py-setuptools", type="build")
-    depends_on("py-msrest@0.5.0:", type=("build", "run"))
+
     depends_on("py-msrestazure@0.4.32:1", type=("build", "run"))
     depends_on("py-azure-common@1.1:1", type=("build", "run"))
+
+    with when("@:12"):
+        depends_on("py-msrest@0.6.21:", when="@11:", type=("build", "run"))
+        depends_on("py-msrest@0.5.0:", type=("build", "run"))

var/spack/repos/builtin/packages/py-azure-core/package.py

@@ -15,14 +15,21 @@ class PyAzureCore(PythonPackage):
 
     license("MIT")
 
+    version("1.29.2", sha256="beb0fe88d1043d8457318e8fb841d9caa648211092eda213c16b376401f3710d")
+    version("1.28.0", sha256="e9eefc66fc1fde56dab6f04d4e5d12c60754d5a9fa49bdcfd8534fc96ed936bd")
+    version("1.27.1", sha256="5975c20808fa388243f01a8b79021bfbe114f503a27c543f002c5fc8bbdd73dd")
+    version("1.26.4", sha256="075fe06b74c3007950dd93d49440c2f3430fd9b4a5a2756ec8c79454afc989c6")
     version("1.26.1", sha256="223b0e90cbdd1f03c41b195b03239899843f20d00964dbb85e64386873414a2d")
     version("1.21.1", sha256="88d2db5cf9a135a7287dc45fdde6b96f9ca62c9567512a3bb3e20e322ce7deb2")
     version("1.7.0", sha256="a66da240a287f447f9867f54ba09ea235895cec13ea38c5f490ce4eedefdd75c")
     version("1.6.0", sha256="d10b74e783cff90d56360e61162afdd22276d62dc9467e657ae866449eae7648")
 
-    # https://github.com/Azure/azure-sdk-for-python/blob/main/sdk/core/azure-core/setup.py
+    # https://github.com/Azure/azure-sdk-for-python/blob/azure-core_1.29.2/sdk/core/azure-core/setup.py
+
     depends_on("py-setuptools", type="build")
     depends_on("py-requests@2.18.4:", type=("build", "run"))
     depends_on("py-six@1.6:", when="@:1.21", type=("build", "run"))
     depends_on("py-six@1.11:", when="@1.21:", type=("build", "run"))
+    depends_on("py-typing-extensions@4.6:", when="@1.29.2:", type=("build", "run"))
+    depends_on("py-typing-extensions@4.3:", when="@1.26.4:", type=("build", "run"))
     depends_on("py-typing-extensions@4.0.1:", when="@1.26:", type=("build", "run"))

var/spack/repos/builtin/packages/py-azure-identity/package.py

@@ -21,18 +21,23 @@ class PyAzureIdentity(PythonPackage):
 
     license("MIT")
 
+    version("1.14.1", sha256="48e2a9dbdc59b4f095f841d867d9a8cbe4c1cdbbad8251e055561afd47b4a9b8")
+    version("1.13.0", sha256="c931c27301ffa86b07b4dcf574e29da73e3deba9ab5d1fe4f445bb6a3117e260")
     version("1.12.0", sha256="7f9b1ae7d97ea7af3f38dd09305e19ab81a1e16ab66ea186b6579d85c1ca2347")
     version("1.3.1", sha256="5a59c36b4b05bdaec455c390feda71b6495fc828246593404351b9a41c2e877a")
     version("1.2.0", sha256="b32acd1cdb6202bfe10d9a0858dc463d8960295da70ae18097eb3b85ab12cb91")
 
-    # https://github.com/Azure/azure-sdk-for-python/blob/azure-identity_1.12.0/sdk/identity/azure-identity/setup.py
+    # https://github.com/Azure/azure-sdk-for-python/blob/azure-identity_1.14.1/sdk/identity/azure-identity/setup.py
+
     depends_on("py-setuptools", type="build")
+
     with when("@1.12:"):
         depends_on("py-azure-core@1.11:1", type=("build", "run"))
         depends_on("py-cryptography@2.5:", type=("build", "run"))
+        depends_on("py-msal@1.20:1", type=("build", "run"), when="@1.13:")
         depends_on("py-msal@1.12:1", type=("build", "run"))
         depends_on("py-msal-extensions@0.3:1", type=("build", "run"))
-        depends_on("py-six@1.12:", type=("build", "run"))
+        depends_on("py-six@1.12:", type=("build", "run"), when="@1.12")
 
     with when("@:1.11"):
         depends_on("py-azure-core@1", type=("build", "run"))

var/spack/repos/builtin/packages/py-azure-mgmt-batch/package.py

@@ -11,11 +11,28 @@ class PyAzureMgmtBatch(PythonPackage):
     """Microsoft Azure Batch Management Client Library for Python."""
 
     homepage = "https://github.com/Azure/azure-sdk-for-python"
-    pypi = "azure-mgmt-batch/azure-mgmt-batch-9.0.0.zip"
+    pypi = "azure-mgmt-batch/azure-mgmt-batch-17.1.0.zip"
 
+    version("17.1.0", sha256="385bf920898dc2d5807865fbe45019f10cdfbef651c6dbfa4745a842525dbafb")
+    version("16.2.0", sha256="69691066cd5a2c86e8fdaaefbb80e2940381acedfc8053df193b5214d2ece682")
+    version("15.0.0", sha256="9b793bb31a0d4dc8c29186db61db24d83795851a75846aadb187cf95bf853ccb")
+    version("14.0.0", sha256="1d3b2c9ebd57c8874e11d29e7dd05a1f078d2156fc9683e2f2ad41024e448bf6")
+    version("10.0.1", sha256="455e2f1010a59163bfd25d72e9d8dc7847df566795bc35655bcb2de925763d33")
     version("9.0.0", sha256="03417eecfa1fac906e674cb1cb43ed7da27a96277277b091d7c389ba39f6c3fe")
 
+    # https://github.com/Azure/azure-sdk-for-python/blob/azure-mgmt-batch_14.0.0/sdk/batch/azure-mgmt-batch/setup.py
+
     depends_on("py-setuptools", type="build")
-    depends_on("py-msrest@0.5.0:", type=("build", "run"))
-    depends_on("py-msrestazure@0.4.32:1", type=("build", "run"))
+
+    depends_on("py-isodate@0.6.1:0", type=("build", "run"), when="@17.1:")
     depends_on("py-azure-common@1.1:1", type=("build", "run"))
+    depends_on("py-azure-mgmt-core@1.2:1", type=("build", "run"), when="@14:")
+    depends_on("py-azure-mgmt-core@1.3:1", type=("build", "run"), when="@16.1:")
+    depends_on("py-azure-mgmt-core@1.3.2:1", type=("build", "run"), when="@17:")
+
+    with when("@:17.0"):
+        depends_on("py-msrest@0.5.0:", type=("build", "run"))
+        depends_on("py-msrest@0.6.21:", type=("build", "run"), when="@16:")
+        depends_on("py-msrest@0.7.1:", type=("build", "run"), when="@17:")
+
+    depends_on("py-msrestazure@0.4.32:1", type=("build", "run"), when="@:10")

var/spack/repos/builtin/packages/py-azure-mgmt-core/package.py

@@ -15,9 +15,20 @@ class PyAzureMgmtCore(PythonPackage):
 
     license("MIT")
 
+    version("1.4.0", sha256="d195208340094f98e5a6661b781cde6f6a051e79ce317caabd8ff97030a9b3ae")
+    version("1.3.2", sha256="07f4afe823a55d704b048d61edfdc1318c051ed59f244032126350be95e9d501")
+    version("1.2.2", sha256="4246810996107f72482a9351cf918d380c257e90942144ec9c0c2abda1d0a312")
     version("1.2.0", sha256="8fe3b59446438f27e34f7b24ea692a982034d9e734617ca1320eedeee1939998")
     version("1.0.0", sha256="510faf49a10daec8346cc086143d8e667ef3b4f8c8022a8e710091027631a55e")
 
+    # https://github.com/Azure/azure-sdk-for-python/blob/azure-mgmt-core_1.4.0/sdk/core/azure-mgmt-core/setup.py
+
     depends_on("py-setuptools", type="build")
+    depends_on("py-azure-core@1.26.2:1", when="@1.4.0:", type=("build", "run"))
+    depends_on("py-azure-core@1.24:1", when="@1.3.2:", type=("build", "run"))
+    depends_on("py-azure-core@1.23:1", when="@1.3.1:", type=("build", "run"))
+    depends_on("py-azure-core@1.15:1", when="@1.3:", type=("build", "run"))
+    depends_on("py-azure-core@1.9:1", when="@1.2.2:", type=("build", "run"))
+    depends_on("py-azure-core@1.8.2:1", when="@1.2.1:", type=("build", "run"))
     depends_on("py-azure-core@1.7.0:1", when="@1.2:", type=("build", "run"))
     depends_on("py-azure-core@1.4.0:1", type=("build", "run"))

var/spack/repos/builtin/packages/py-azure-storage-blob/package.py

@@ -3,6 +3,7 @@
 #
 # SPDX-License-Identifier: (Apache-2.0 OR MIT)
 
+
 from spack.package import *
 
 
@@ -15,9 +16,31 @@ class PyAzureStorageBlob(PythonPackage):
 
     license("MIT")
 
+    version("12.17.0", sha256="c14b785a17050b30fc326a315bdae6bc4a078855f4f94a4c303ad74a48dc8c63")
+    version("12.16.0", sha256="43b45f19a518a5c6895632f263b3825ebc23574f25cc84b66e1630a6160e466f")
+    version("12.15.0", sha256="f8b8d582492740ab16744455408342fb8e4c8897b64a8a3fc31743844722c2f2")
+    version("12.14.0", sha256="a72dd9923e4b38a552f2bc1749d1fa5b820f497a8fb3cd2d77e7045bbe87bb4d")
+    version("12.13.1", sha256="899c4b8e2671812d2cf78f107556a27dbb128caaa2bb06094e72a3d5836740af")
+    version("12.12.0", sha256="f6daf07d1ca86d189ae15c9b1859dff5b7127bf24a07a4bbe41e0b81e01d62f7")
+    version("12.11.0", sha256="49535b3190bb69d0d9ff7a383246b14da4d2b1bdff60cae5f9173920c67ca7ee")
+    version("12.10.0", sha256="3c7dc2c93e7ff2a731acd66a36a1f0a6266072b4154deba4894dab891285ea3a")
     version("12.9.0", sha256="cff66a115c73c90e496c8c8b3026898a3ce64100840276e9245434e28a864225")
 
+    # https://github.com/Azure/azure-sdk-for-python/blob/azure-storage-blob_12.17.0/sdk/storage/azure-storage-blob/setup.py
+
     depends_on("py-setuptools", type="build")
+
+    depends_on("py-azure-core@1.28:1", type=("build", "run"), when="@12.17:")
+    depends_on("py-azure-core@1.26:1", type=("build", "run"), when="@12.15:")
+    depends_on("py-azure-core@1.24.2:1", type=("build", "run"), when="@12.14:")
+    depends_on("py-azure-core@1.23.1:1", type=("build", "run"), when="@12.12:")
+    depends_on("py-azure-core@1.15:1", type=("build", "run"), when="@12.10:")
     depends_on("py-azure-core@1.10:1", type=("build", "run"))
-    depends_on("py-msrest@0.6.21:", type=("build", "run"))
     depends_on("py-cryptography@2.1.4:", type=("build", "run"))
+    depends_on("py-typing-extensions@4.3:", type=("build", "run"), when="@12.17:")
+    depends_on("py-typing-extensions@4.0.1:", type=("build", "run"), when="@12.15:")
+    depends_on("py-isodate@0.6.1:", type=("build", "run"), when="@12.15:")
+
+    with when("@:12.14"):
+        depends_on("py-msrest@0.7.1:", type=("build", "run"), when="@12.14:")
+        depends_on("py-msrest@0.6.21:", type=("build", "run"))

var/spack/repos/builtin/packages/py-biobb-structure-utils/package.py

@@ -0,0 +1,25 @@
+# Copyright 2013-2024 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack.package import *
+
+
+class PyBiobbStructureUtils(PythonPackage):
+    """Biobb_structure_utils is the Biobb module collection to modify or extract information
+    from a PDB structure file, such as pulling out a particular model or chain, removing water
+    molecules or ligands, or renumbering or sorting atoms or residues"""
+
+    pypi = "biobb_structure_utils/biobb_structure_utils-4.1.0.tar.gz"
+
+    maintainers("d-beltran")
+
+    # Versions
+    version("4.1.0", sha256="07c6268e2f40de595325aaf88839dd180950ba5bd7e51acbf726a9b982fe69cd")
+
+    # Dependencies
+    depends_on("py-setuptools", type="build")
+    depends_on("python@3.8:", type=("build", "run"))
+    depends_on("py-biobb-common@4.1.0", type=("build", "run"))
+    depends_on("py-biobb-structure-checking@3.13.4", type=("build", "run"))

var/spack/repos/builtin/packages/py-charm4py/package.py

@@ -36,7 +36,7 @@ class PyCharm4py(PythonPackage):
     depends_on("py-setuptools", type="build")
     # in newer pip versions --install-option does not exist
     depends_on("py-pip@:23.0", type="build")
-    depends_on("py-cython", type="build")
+    depends_on("py-cython@:2", type="build")
     depends_on("py-cffi@1.7:", type="build")
     depends_on("py-numpy@1.10.0:", type=("build", "run"))
     depends_on("py-greenlet", type=("build", "run"))

var/spack/repos/builtin/packages/py-kubernetes/package.py

@@ -18,6 +18,10 @@ class PyKubernetes(PythonPackage):
 
     license("Apache-2.0")
 
+    version("29.0.0", sha256="c4812e227ae74d07d53c88293e564e54b850452715a59a927e7e1bc6b9a60459")
+    version("28.1.0", sha256="1468069a573430fb1cb5ad22876868f57977930f80a6749405da31cd6086a7e9")
+    version("27.2.0", sha256="d479931c6f37561dbfdf28fc5f46384b1cb8b28f9db344ed4a232ce91990825a")
+    version("26.1.0", sha256="5854b0c508e8d217ca205591384ab58389abdae608576f9c9afc35a3c76a366c")
     version("25.3.0", sha256="213befbb4e5aed95f94950c7eed0c2322fc5a2f8f40932e58d28fdd42d90836c")
     version("21.7.0", sha256="c9849afc2eafdce60efa210049ee7a94e7ef6cf3a7afa14a69b3bf0447825977")
     version("20.13.0", sha256="ce5e881c13dc56f21a243804f90bc3c507af93c380f505c00e392c823968e4de")
@@ -31,7 +35,6 @@ class PyKubernetes(PythonPackage):
     version("10.0.1", sha256="3770a496663396ad1def665eeadb947b3f45217a08b64b10c01a57e981ac8592")
     version("9.0.0", sha256="a8b0aed55ba946faea660712595a52ae53a8854df773d96f47a63fa0c9d4e3bf")
 
-    depends_on("python@3.6:", type=("build", "run"))
     depends_on("py-certifi@14.05.14:", type=("build", "run"))
     depends_on("py-six@1.9.0:", type=("build", "run"))
     depends_on("py-python-dateutil@2.5.3:", type=("build", "run"))
@@ -42,4 +45,6 @@ class PyKubernetes(PythonPackage):
     depends_on("py-websocket-client@0.32:0.39,0.43:", type=("build", "run"))
     depends_on("py-requests", type=("build", "run"))
     depends_on("py-requests-oauthlib", type=("build", "run"))
+    depends_on("py-oauthlib@3.2.2:", type=("build", "run"), when="@27.2:")
+    depends_on("py-urllib3@1.24.2:1", type=("build", "run"), when="@28.1.0")
     depends_on("py-urllib3@1.24.2:", type=("build", "run"))

var/spack/repos/builtin/packages/py-metric-learn/package.py

@@ -0,0 +1,26 @@
+# Copyright 2013-2024 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack.package import *
+
+
+class PyMetricLearn(PythonPackage):
+    """metric-learn contains efficient Python implementations of several
+    popular supervised and weakly-supervised metric learning algorithms. As
+    part of scikit-learn-contrib, the API of metric-learn is compatible with
+    scikit-learn, the leading library for machine learning in Python. This
+    allows to use all the scikit-learn routines (for pipelining, model
+    selection, etc) with metric learning algorithms through a unified
+    interface."""
+
+    homepage = "https://github.com/scikit-learn-contrib/metric-learn"
+    pypi = "metric-learn/metric-learn-0.7.0.tar.gz"
+
+    version("0.7.0", sha256="2b35246a1098d74163b16cc7779e0abfcbf9036050f4caa258e4fee55eb299cc")
+
+    depends_on("py-setuptools", type="build")
+    depends_on("py-numpy@1.11.0:", type=("build", "run"))
+    depends_on("py-scipy@0.17.0:", type=("build", "run"))
+    depends_on("py-scikit-learn@0.21.3:", type=("build", "run"))

var/spack/repos/builtin/packages/py-minisom/package.py

@@ -0,0 +1,30 @@
+# Copyright 2013-2024 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack.package import *
+
+
+class PyMinisom(PythonPackage):
+    """MiniSom is a minimalistic and Numpy based implementation of the Self
+    Organizing Maps (SOM). SOM is a type of Artificial Neural Network able to
+    convert complex, nonlinear statistical relationships between
+    high-dimensional data items into simple geometric relationships on a
+    low-dimensional display. Minisom is designed to allow researchers to easily
+    build on top of it and to give students the ability to quickly grasp its
+    details.
+
+    The project initially aimed for a minimalistic implementation of the
+    Self-Organizing Map (SOM) algorithm, focusing on simplicity in features,
+    dependencies, and code style. Although it has expanded in terms of
+    features, it remains minimalistic by relying only on the numpy library and
+    emphasizing vectorization in coding style."""
+
+    homepage = "https://github.com/JustGlowing/minisom"
+    pypi = "MiniSom/MiniSom-2.3.1.tar.gz"
+
+    version("2.3.1", sha256="c0f1411616d7614fbd440a811975c12c7dfc091baea33efb49f5f4eabad7b966")
+
+    depends_on("py-numpy", type=("build", "run"))
+    depends_on("py-setuptools", type=("build"))

var/spack/repos/builtin/packages/py-msrest/package.py

@@ -11,8 +11,15 @@ class PyMsrest(PythonPackage):
     """AutoRest swagger generator Python client runtime."""
 
     homepage = "https://github.com/Azure/msrest-for-python"
-    pypi = "msrest/msrest-0.6.16.tar.gz"
+    pypi = "msrest/msrest-0.7.1.zip"
 
+    def url_for_version(self, version):
+        if Version("0.4.8") < version < Version("0.7"):
+            return "https://pypi.io/packages/source/m/msrest/msrest-{0}.tar.gz".format(version)
+
+        return super().url_for_version(version)
+
+    version("0.7.1", sha256="6e7661f46f3afd88b75667b7187a92829924446c7ea1d169be8c4bb7eeb788b9")
     version("0.6.21", sha256="72661bc7bedc2dc2040e8f170b6e9ef226ee6d3892e01affd4d26b06474d68d8")
     version("0.6.16", sha256="214c5be98954cb45feb6a6a858a7ae6d41a664e80294b65db225bbaa33d9ca3c")
 
@@ -21,3 +28,4 @@ class PyMsrest(PythonPackage):
     depends_on("py-requests-oauthlib@0.5.0:", type=("build", "run"))
     depends_on("py-isodate@0.6.0:", type=("build", "run"))
     depends_on("py-certifi@2017.4.17:", type=("build", "run"))
+    depends_on("py-azure-core@1.24:", type=("build", "run"), when="@0.7.1:")

var/spack/repos/builtin/packages/py-oauthlib/package.py

@@ -17,6 +17,7 @@ class PyOauthlib(PythonPackage):
 
     license("BSD-3-Clause")
 
+    version("3.2.2", sha256="9859c40929662bec5d64f34d01c99e093149682a3f38915dc0655d5a633dd918")
     version("3.2.1", sha256="1565237372795bf6ee3e5aba5e2a85bd5a65d0e2aa5c628b9a97b7d7a0da3721")
     version("3.1.1", sha256="8f0215fcc533dd8dd1bee6f4c412d4f0cd7297307d43ac61666389e3bc3198a3")
     version("3.1.0", sha256="bee41cc35fcca6e988463cacc3bcb8a96224f470ca547e697b604cc697b2f889")

var/spack/repos/builtin/packages/py-smote-variants/package.py

@@ -0,0 +1,35 @@
+# Copyright 2013-2024 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack.package import *
+
+
+class PySmoteVariants(PythonPackage):
+    """Variants of the synthetic minority oversampling technique (SMOTE) for
+    imbalanced learning"""
+
+    homepage = "https://github.com/analyticalmindsltd/smote_variants"
+    pypi = "smote_variants/smote_variants-0.7.3.tar.gz"
+
+    version("0.7.3", sha256="69497c764f101a76e8a3d4a9c80176704375c7aa5e26914f19222b59fb03b890")
+
+    depends_on("python@3.5:", type=("build", "run"))
+
+    depends_on("py-wheel@0.33.4:", type="build")
+    depends_on("py-setuptools@41.0.1:", type="build")
+    depends_on("py-pytest-runner", type="build")
+
+    depends_on("py-numpy", type=("build", "run"))
+    depends_on("py-scipy", type=("build", "run"))
+    depends_on("py-scikit-learn", type=("build", "run"))
+    depends_on("py-joblib", type=("build", "run"))
+    depends_on("py-minisom", type=("build", "run"))
+    depends_on("py-tensorflow", type=("build", "run"))
+    depends_on("py-keras", type=("build", "run"))
+    depends_on("py-pandas", type=("build", "run"))
+    depends_on("mkl")
+    depends_on("py-metric-learn", type=("build", "run"))
+    depends_on("py-seaborn", type=("build", "run"))
+    # Not including statistics, because is only needed for python 2