Rearrange dependencies, make some optional

.github/workflows/unittest.yml

@@ -18,18 +18,6 @@ jobs:
       matrix:
         os: [ubuntu-latest, windows-latest, macos-latest]
         python-version: [3.8, 3.9, "3.10", "3.11"]
-        # exclude:
-        #   # excludes py38 on macOS, which seems to stall currently
-        #   - os: macos-latest
-        #     python-version: 3.8
-        #   - os: macos-latest
-        #     python-version: 3.9
-        #   - os: macos-latest
-        #     python-version: "3.10"
-        #   - os: macos-latest
-        #     python-version: "3.11"
-        #   - os: windows-latest
-        #     python-version: "3.11"
     steps:
       - uses: actions/checkout@v3
       - uses: actions/setup-python@v4

environment.yml

@@ -20,7 +20,6 @@ dependencies:
   - tinydb
   - periodictable
   - mpltern>=0.4.0
-  - mpmath
   - sympy>=1.7 # import changes after sympy 1.6
   - joblib
   - requests
@@ -35,8 +34,6 @@ dependencies:
   - pip
   - black
   - isort
-  - jedi<0.18.0 # for use on atom/ipython
-  - pyzmq
   - pytest
   - pytest-runner
   - pytest-cov

pyrolite/util/spatial.py

@@ -4,7 +4,11 @@
 import itertools
 
 import numpy as np
-from psutil import virtual_memory  # memory check
+
+try:
+    from psutil import virtual_memory  # memory check
+except ImportError:
+    virtual_memory = None
 
 from .log import Handle
 
@@ -176,14 +180,16 @@ def great_circle_distance(
         # but, with large arrays it'll spit out a memory error
         # so instead we can try to build it numerically
         size = np.max([a.shape[0] for a in [φ1, φ2, λ1, λ2]])
-        mem = virtual_memory().total  # total physical memory available
         estimated_matrix_size = np.array([[1.0]], dtype=dtype).nbytes * size**2
         logger.debug(
             "Attempting to build {}x{} array of size {:.2f} Gb.".format(
                 size, size, estimated_matrix_size / 1024**3
             )
         )
-        if estimated_matrix_size > (mem * max_memory_fraction):
+
+        infeasible = estimated_matrix_size > (virtual_memory().total * max_memory_fraction) if virtual_memory is not None else False
+
+        if infeasible:
             logger.warn(
                 "Angle array for segmented distance matrix larger than maximum memory "
                 "fraction, computing mean global distances instead."

setup.py

@@ -15,9 +15,10 @@
 ]
 dev_require = ["pytest", "versioneer", "black", "isort", "twine"] + tests_require + docs_require
 db_require = ["pyodbc", "psycopg2"]
-skl_require = ["scikit-learn"]
+skl_require = ["scikit-learn",        "joblib"]
 stats_require = ["statsmodels", "scikit-learn"]
-spatial_require = ["owslib", "geojson"]  # this needs pyproj -> C compiler
+spatial_require = ["owslib", "geojson", "psutil"]  # this needs pyproj -> C compiler
+excel_require = ["xlrd", "openpyxl"]  # reading excel from pandas, writing excel from pandas
 
 with open("README.md", "r") as src:
     LONG_DESCRIPTION = src.read()
@@ -56,18 +57,12 @@
         "numpy",
         "numpydoc",
         "tinydb>4.1",  # >4.1 required for read-only access mode for JSON storage
-        "typing-extensions",  # required for newer tinydb versions?
-        "psutil",
         "periodictable",
         "matplotlib",
         "mpltern>=0.4.0",
         "scipy>=1.2",  # uses scipy.optimize.Bounds, added around 1.2
-        "mpmath",
         "sympy>=1.7",
         "pandas>=1.0",  # dataframe acccessors, attrs attribute
-        "xlrd",  # reading excel from pandas
-        "openpyxl",  # writing excel from pandas
-        "joblib",
         "requests",  # used by alphaMELTS utilities,  util.web
     ],
     extras_require={
@@ -77,6 +72,7 @@
         "spatial": spatial_require,
         "db": db_require,
         "stats": stats_require,
+        "excel": excel_require
     },
     tests_require=tests_require,
     test_suite="test",