Merge pull request #215 from loriab/psiapi_detection

psithon and psiapi

README.md

@@ -1,7 +1,7 @@
 QCEngine
 ========
 [![Travis Build Status](https://travis-ci.org/MolSSI/QCEngine.png)](https://travis-ci.org/MolSSI/QCEngine)
-[![codecov](https://codecov.io/gh/MolSSI/QCEngine/branch/master/graph/badge.svg)](https://codecov.io/gh/MolSSI/QCEngine/branch/master)
+[![codecov](https://img.shields.io/codecov/c/github/MolSSI/QCEngine.svg?logo=Codecov&logoColor=white)](https://codecov.io/gh/MolSSI/QCEngine)
 [![Azure Build Status](https://dev.azure.com/MolSSI/QCArchive/_apis/build/status/MolSSI.QCEngine?branchName=master)](https://dev.azure.com/MolSSI/QCArchive/_build/latest?definitionId=5&branchName=master)
 [![Language grade: Python](https://img.shields.io/lgtm/grade/python/g/MolSSI/QCEngine.svg?logo=lgtm&logoWidth=18)](https://lgtm.com/projects/g/MolSSI/QCEngine/context:python)
 [![Documentation Status](https://readthedocs.org/projects/qcengine/badge/?version=latest)](https://qcengine.readthedocs.io/en/latest/?badge=latest)

docs/source/changelog.rst

@@ -1,8 +1,8 @@
 Changelog
 =========
 
-.. vX.Y.0 / 2019-MM-DD
-.. -------------------
+.. vX.Y.0 / 2020-MM-DD
+.. --------------------
 ..
 .. New Features
 .. ++++++++++++
@@ -13,6 +13,23 @@ Changelog
 .. Bug Fixes
 .. +++++++++
 
+
+v0.14.0 / 2020-MM-DD
+--------------------
+
+New Features
+++++++++++++
+
+Enhancements
+++++++++++++
+-(:pr:`215`) Psi4 - indicating location by either PATH or PYTHONPATH sets up both subprocess and API execution.
+-(:pr:`215`) ``get_program`` shows the helpful "install this" messages from ``found()`` rather than just saying "cannot be found".
+
+Bug Fixes
++++++++++
+-(:pr:`215`) NWChem complains *before* a calculation if the necessary ``networkx`` package not available.
+
+
 v0.13.0 / 2019-12-10
 --------------------
 

qcengine/cli.py

@@ -75,8 +75,8 @@ def info_version():
  import qcelemental
 
  print(">>> Version information")
- print(f"QCEngine version: {__version__}")
- print(f"QCElemental version: {qcelemental.__version__}")
+ print(f"QCEngine: {__version__}")
+ print(f"QCElemental: {qcelemental.__version__}")
  print()
 
  def info_programs(): # lgtm: [py/similar-function]
@@ -88,12 +88,16 @@ def info_programs(): # lgtm: [py/similar-function]
  version = get_program(prog_name).get_version()
  if version is None:
  version = "???"
- print(f"{prog_name} v{version}")
+ print(f"{prog_name + ':':12} v{version}")
 
  print()
  print("Other supported programs:")
  print(" ".join(sorted(all_progs - avail_progs)))
  print()
+ print(
+ """If you think available programs are missing, query for details: `python -c "import qcengine as qcng; qcng.get_program('<program>')"`"""
+ )
+ print()
 
  def info_procedures(): # lgtm: [py/similar-function]
  print(">>> Procedure information")

qcengine/programs/base.py

@@ -66,8 +66,11 @@ def get_program(name: str, check: bool = True) -> "ProgramHarness":
  raise InputError(f"Program {name} is not registered to QCEngine.")
 
  ret = programs[name]
- if check and not ret.found():
- raise ResourceError(f"Program {name} is registered with QCEngine, but cannot be found.")
+ if check:
+ try:
+ ret.found(raise_error=True)
+ except ModuleNotFoundError as err:
+ raise ResourceError(f"Program {name} is registered with QCEngine, but cannot be found.") from err
 
  return ret
 
@@ -103,7 +106,7 @@ def list_available_programs() -> Set[str]:
 register_program(TeraChemHarness())
 register_program(TurbomoleHarness())
 
-# Semi-emperical
+# Semi-empirical
 register_program(MopacHarness())
 
 # AI

qcengine/programs/nwchem/runner.py

@@ -11,7 +11,7 @@
 import numpy as np
 import qcelemental as qcel
 from qcelemental.models import AtomicResult, Provenance, AtomicInput
-from qcelemental.util import safe_version, which
+from qcelemental.util import safe_version, which, which_import
 
 from qcengine.config import TaskConfig, get_config
 from qcengine.exceptions import UnknownError
@@ -52,13 +52,22 @@ class Config(ProgramHarness.Config):
 
  @staticmethod
  def found(raise_error: bool = False) -> bool:
- return which(
+ qc = which(
  "nwchem",
  return_bool=True,
  raise_error=raise_error,
  raise_msg="Please install via http:https://www.nwchem-sw.org/index.php/Download",
  )
 
+ dep = which_import(
+ "networkx",
+ return_bool=True,
+ raise_error=raise_error,
+ raise_msg="For NWChem harness, please install via `conda install networkx -c conda-forge`.",
+ )
+
+ return qc and dep
+
  def get_version(self) -> str:
  self.found(raise_error=True)
 

qcengine/programs/psi4.py

@@ -3,14 +3,16 @@
 """
 import json
 import os
+import sys
+from pathlib import Path
 from typing import Dict, TYPE_CHECKING
 
 if TYPE_CHECKING:
  from ..config import TaskConfig
  from qcelemental.models import AtomicInput
 
 from qcelemental.models import AtomicResult
-from qcelemental.util import deserialize, parse_version, safe_version, which
+from qcelemental.util import deserialize, parse_version, safe_version, which, which_import
 
 from ..exceptions import InputError, RandomError, ResourceError, UnknownError
 from ..util import execute, popen, temporary_directory
@@ -34,6 +36,28 @@ class Config(ProgramHarness.Config):
 
  @staticmethod
  def found(raise_error: bool = False) -> bool:
+ psithon = which("psi4", return_bool=True)
+ psiapi = which_import("psi4", return_bool=True)
+
+ if psithon and not psiapi:
+ with popen([which("psi4"), "--pythonpath"]) as exc:
+ exc["proc"].wait(timeout=30)
+ if "pythonpath does not exist" in exc["stderr"]:
+ pass
+ else:
+ sys.path.append(exc["stdout"].split()[-1])
+
+ if psiapi and not psithon:
+ psiimport = str(Path(which_import("psi4")).parent.parent)
+ env = os.environ.copy()
+ env["PYTHONPATH"] = psiimport
+ with popen(["python", "-c", "import psi4; print(psi4.executable[:-5])"], popen_kwargs={"env": env}) as exc:
+ exc["proc"].wait(timeout=30)
+ os.environ["PATH"] += os.pathsep + exc["stdout"].split()[-1]
+
+ if psithon or psiapi:
+ return True
+
  return which(
  "psi4",
  return_bool=True,