From 41c2ea42bdac0840a9bdbc42be0bf12917050416 Mon Sep 17 00:00:00 2001
From: stefanch <AG4WobAiWsb8im>
Date: Thu, 4 Feb 2021 14:34:17 +0100
Subject: [PATCH] bugfix

---
 .gitignore        |  1 +
 README.md         |  4 ++--
 setup.py          |  1 -
 sgdml/__init__.py |  2 +-
 sgdml/cli.py      | 36 ++++++++----------------------------
 sgdml/train.py    |  8 +++++++-
 6 files changed, 19 insertions(+), 33 deletions(-)

diff --git a/.gitignore b/.gitignore
index 0518e12..6a6df3b 100644
--- a/.gitignore
+++ b/.gitignore
@@ -10,3 +10,4 @@
 # Python egg metadata, regenerated from source files by setuptools.
 /*.egg-info
 /*.egg
+sgdml/_bmark_cache.npz
diff --git a/README.md b/README.md
index d3e48a1..77b87d8 100644
--- a/README.md
+++ b/README.md
@@ -5,13 +5,13 @@ For more details visit: [http://sgdml.org/](http://sgdml.org/)
 Documentation can be found here: [http://sgdml.org/doc/](http://sgdml.org/doc/)
 
 #### Requirements:
-- Python 2.7/3.7+
+- Python 3.7+
 - NumPy (>=1.19)
 - SciPy (>=1.1)
 
 #### Optional:
 - PyTorch (for GPU acceleration)
-- ASE (to run atomistic simulations)
+- ASE (>=3.16.2) (to run atomistic simulations)
 
 ## Getting started
 
diff --git a/setup.py b/setup.py
index 2a7f949..c10ac0a 100644
--- a/setup.py
+++ b/setup.py
@@ -40,7 +40,6 @@ def get_property(property, package):
         'License :: OSI Approved :: MIT License',
         'Operating System :: MacOS :: MacOS X',
         'Operating System :: POSIX :: Linux',
-        'Programming Language :: Python :: 2.7',
         'Programming Language :: Python :: 3.7',
         'Topic :: Scientific/Engineering :: Chemistry',
         'Topic :: Scientific/Engineering :: Physics',
diff --git a/sgdml/__init__.py b/sgdml/__init__.py
index d9480cf..fcda3e5 100755
--- a/sgdml/__init__.py
+++ b/sgdml/__init__.py
@@ -22,7 +22,7 @@
 # OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
 # SOFTWARE.
 
-__version__ = '0.4.10.dev2'
+__version__ = '0.4.10'
 
 MAX_PRINT_WIDTH = 100
 LOG_LEVELNAME_WIDTH = 7  # do not modify
diff --git a/sgdml/cli.py b/sgdml/cli.py
index 94b098d..08e5e81 100644
--- a/sgdml/cli.py
+++ b/sgdml/cli.py
@@ -1833,34 +1833,7 @@ def _add_argument_dir_with_file_type(parser, type, or_file=False):
             help='user-defined model output file name',
         )
 
-    for subparser in [parser_all, parser_create]:
-        group = subparser.add_mutually_exclusive_group()
-        group.add_argument(
-            '--cg',
-            dest='use_cg',
-            action='store_true',
-            help='use iterative solver (conjugate gradient) with Nystroem preconditioner',
-            # help=argparse.SUPPRESS
-        )
-        subparser.add_argument(
-            '--ip',
-            dest='n_inducing_pts_init',
-            metavar='<n_inducing_pts_init>',
-            type=io.is_strict_pos_int,
-            help='initial number of inducing points (<= n_train) to use for preconditioner matrix (default: 25, larger value: fewer iterations, but higher per-iteration memory and processing cost)',
-            nargs='?',
-            default=25,
-        )
-        subparser.add_argument(
-            '--coff',
-            dest='interact_cut_off',
-            metavar='<interact_cut_off>',
-            type=io.is_strict_pos_int,
-            help='decay pairwise interactions to zero from a given distance (localizes the model)',
-            nargs='?',
-            default=None,
-        )
-
+    
     # train
     _add_argument_dir_with_file_type(parser_train, 'task', or_file=True)
 
@@ -1935,6 +1908,13 @@ def _add_argument_dir_with_file_type(parser, type, or_file=False):
         args['solver'] = 'cg'
     args.pop('use_cg', None)
 
+
+    # TODO: remove dummy variables once iterative solver ships
+    missing_keys = ['n_inducing_pts_init', 'interact_cut_off', 'use_cg']
+    for missing_key in missing_keys:
+        if missing_key not in args: 
+            args[missing_key] = None
+
     try:
         getattr(sys.modules[__name__], args['command'])(**args)
     except AssistantError as err:
diff --git a/sgdml/train.py b/sgdml/train.py
index 36ca79d..97608ef 100755
--- a/sgdml/train.py
+++ b/sgdml/train.py
@@ -47,7 +47,13 @@
 
 from . import __version__, DONE, NOT_DONE
 from .solvers.analytic import Analytic
-from .solvers.iterative import Iterative
+
+# TODO: remove exception handling once iterative solver ships
+try:
+    from .solvers.iterative import Iterative
+except ImportError:
+    pass
+
 from .predict import GDMLPredict
 from .utils.desc import Desc
 from .utils import io, perm, ui