Fix numpy bug with alen()

* The numpy.alen() function is deprecated. We use len() instead
* The use of pkg_resources is discouraged. We use importlib.metadata
  instead. I also removed setuptools_scm get_version. I switch to
  a simple call to "git describe", easier now that we use git flow
* The build fails with python3.10 if compiling wx from sources.
  A fix in the Makefile will be proposed in a future commit.

Makefile

@@ -41,6 +41,8 @@ _build_wx/wxPython.target:
 	@$(INSIDE_VENV) echo "Building wxPython for your `python --version 2>&1` under Linux $(DISTRO_RELEASE)..."
 	# Create a folder to build wx into
 	@mkdir -p _build_wx
+	@$(INSIDE_VENV) pip install attrdict sip
+	# TODO: attrdict is no longer compatible with collections package. The build will fail
 	# download the wheel or the source if it cannot find a wheel
 	@$(INSIDE_VENV) cd _build_wx && pip download -f https://extras.wxpython.org/wxPython4/extras/linux/gtk3/$(DISTRO_RELEASE) wxPython
 	# Build the source if a tar.gz was downloaded

src/msspec/utils.py

@@ -18,8 +18,8 @@
 # along with this msspec.  If not, see <http://www.gnu.org/licenses/>.
 #
 # Source file  : src/msspec/utils.py
-# Last modified: ven. 10 avril 2020 15:49:35
+# Last modified: Thu, 06 Oct 2022 18:19:16 +0200
-# Committed by : "Sylvain Tricot <sylvain.tricot@univ-rennes1.fr>"
+# Committed by : Sylvain Tricot <sylvain.tricot@univ-rennes1.fr> 1665073156 +0200
 
 
 """
@@ -480,7 +480,7 @@ def hemispherical_cluster(cluster, emitter_tag=0, emitter_plane=0, diameter=0,
     a = cell[:, 0].max()    # a lattice parameter
 
     # the number of planes in the cluster
-    p = np.alen(np.unique(np.round(cluster.get_positions()[:, 2], 4)))
+    p = len(np.unique(np.round(cluster.get_positions()[:, 2], 4)))
     # the symbol of your emitter
     symbol = cluster[np.where(cluster.get_tags() == emitter_tag)[0][0]].symbol
 
@@ -585,7 +585,7 @@ def hemispherical_cluster(cluster, emitter_tag=0, emitter_plane=0, diameter=0,
     # an array of all unique remaining z
     all_z = np.sort(np.unique(np.round(cluster.get_positions()[:, 2], 4)))
 
-    assert emitter_plane < np.alen(all_z), ("There are not enough existing "
+    assert emitter_plane < len(all_z), ("There are not enough existing "
                                             "plans.")
     ze = all_z[- emitter_plane - 1]         # the z-coordinate of the emitter
     Atoms.translate(cluster, [0, 0, -ze])   # put the emitter in (0,0,0)

src/msspec/version.py

@@ -16,39 +16,38 @@
 # along with this msspec.  If not, see <http://www.gnu.org/licenses/>.
 #
 # Source file  : src/msspec/version.py
-# Last modified: ven. 10 avril 2020 17:34:38
+# Last modified: Thu, 06 Oct 2022 18:19:16 +0200
-# Committed by : "Sylvain Tricot <sylvain.tricot@univ-rennes1.fr>"
+# Committed by : Sylvain Tricot <sylvain.tricot@univ-rennes1.fr> 1665073156 +0200
 
 
 import os
 
-from pkg_resources import DistributionNotFound
+from importlib.metadata import version
-from pkg_resources import get_distribution
+import subprocess
-from pkg_resources import parse_version
 
 # find the version number
-# 1- Try to read it from the git info
+# 1- If it fails, try to read it from the distribution file
-# 2- If it fails, try to read it from the distribution file
+# 2- Try to read it from the git info
 # 3- If it fails, try to read it from the VERSION file
 
+PKGNAME = 'msspec'
+
 try:
-    from setuptools_scm import get_version
+    __version__ = version(PKGNAME)
-    v = get_version(root='../../', relative_to=__file__, version_scheme="post-release")
-    v = parse_version(v)
-    if v._version.post[-1] == 0:
-        __version__ = v.base_version
-    else:
-        __version__ = v.public
 except Exception as err:
     try:
-        __version__ = get_distribution(__name__.strip('.version')).version
+        p = subprocess.run(["git", "describe"], capture_output=True, text=True)
+        if p.stdout not in ("", None):
+            __version__ = p.stdout.strip()
+        else:
+            raise NameError("git describe failed!")
     except Exception as err:
         try:
             thisfile_path = os.path.abspath(__file__)
             thisfile_dir = os.path.dirname(thisfile_path)
             versionfile = os.path.join(thisfile_dir, "../VERSION")
             with open(versionfile, "r") as fd:
-                __version__ = fd.readline()
+                __version__ = fd.readline().strip()
         except Exception as err:
             print("Unable to get the version number!")
             __version__ = "9.9.9"

src/options.mk

@@ -41,8 +41,7 @@ F2PYFLAGS_DBG = --debug-capi --debug
 # /!\ DO NOT EDIT BELOW THAT LINE (unlesss you know what you're doing...)      #
 # CORE CONFIGURATION                                                           #
 ################################################################################
-#VERSION:=$(shell python -c "import msspec; print(msspec.__version__)")
+VERSION:=$(shell git describe)
-VERSION:=$(shell git describe|sed 's/-\([[:digit:]]\+\)-.*/\.post\1/')
 VENV_PATH := $(INSTALL_PREFIX)/src/msspec_venv_$(VERSION)