OSBModelValidation 0.2.18__py3-none-any.whl

omv/engines/getbrian1.py

@@ -0,0 +1,42 @@
+import os
+import pip
+from omv.common.inout import inform, check_output
+from omv.engines.utils.wdir import working_dir
+
+
+def check_scipy_dev():
+    try:
+        import scipy
+    except ImportError:
+        # Compiling from source is terribly slow, and requires Blas/Lapack...
+        # print('Installing scipy dev...')
+        # pip.main(['install', 'cython'])
+        # pip.main(['install', 'git+http://github.com/scipy/scipy/'])
+        print(
+            "\n***************************************************************************************"
+        )
+        print("\n* ")
+        print("\n**  ERROR: Brian requires scipy. Please install it manually.")
+        print(
+            "\n**  If running OMV on Travis-CI, see https://github.com/OpenSourceBrain/BrianShowcase/blob/master/.travis.yml."
+        )
+        print("\n* ")
+        print(
+            "\n***************************************************************************************"
+        )
+        raise ImportError
+
+
+def install_brian():
+    install_root = os.environ["HOME"]
+
+    with working_dir(install_root):
+        check_output(["git", "clone", "https://github.com/brian-team/brian.git"])
+        inform("Successfully cloned Brian", indent=2, verbosity=1)
+
+    path = os.path.join(install_root, "brian")
+
+    with working_dir(path):
+        check_output(["git", "checkout", "master"])
+        check_output(["python", "setup.py", "install"])
+        inform("Successfully installed Brian", indent=2, verbosity=1)

omv/engines/getbrian2.py

@@ -0,0 +1,17 @@
+from omv.common.inout import pip_install
+
+from omv.engines.getbrian1 import check_scipy_dev
+
+
+def install_brian2(version):
+    if not version:
+        version = "2.5.3"
+    try:
+        pip_install("brian2", version)
+        import brian2
+
+        m = "Successfully installed Brian2..."
+    except Exception as e:
+        m = "ERROR installing Brian2: " + str(e)
+    finally:
+        print(m)

omv/engines/geteden.py

@@ -0,0 +1,17 @@
+from omv.common.inout import pip_install
+
+DEFAULT_VERSION = "0.2.3"
+
+
+def install_eden(version=None):
+    if not version:
+        version = DEFAULT_VERSION
+    try:
+        pip_install("eden-simulator", version)
+        import eden_simulator
+
+        m = "Successfully installed EDEN..."
+    except Exception as e:
+        m = "ERROR installing EDEN: " + str(e)
+    finally:
+        print(m)

omv/engines/getgenesis.py

@@ -0,0 +1,56 @@
+import os
+from subprocess import check_output as co
+
+from omv.engines.utils.wdir import working_dir
+
+simrc = """
+// .simrc file to go in the home directory of all GENESIS users
+//===========================================================================
+//                         environment variables
+//===========================================================================
+//      SIMPATH - path to search for scripts (includes the startup path)
+//      SIMNOTES - default file for simulator notes
+//===========================================================================
+setenv SIMPATH {getenv HOME}/genesis/genesis2.4gamma-master/src/startup \
+{getenv HOME}/genesis/genesis2.4gamma-master/Scripts/neurokit \
+{getenv HOME}/genesis/genesis2.4gamma-master/Scripts/neurokit/prototypes
+
+// This adds the Xodus 1 compatability library directory to the
+// SIMPATH.  If you are not expecting to use X1compat, you can
+// comment out the following line.
+setenv SIMPATH {getenv SIMPATH} \
+{getenv HOME}/genesis/genesis2.4gamma-master/Scripts/X1compat
+
+setenv SIMNOTES {getenv HOME}/genesis/genesis2.4gamma-master/.notes
+setenv GENESIS_HELP {getenv HOME}/genesis/genesis2.4gamma-master/Doc
+
+//===========================================================================
+//                             set up tables
+//===========================================================================
+schedule// default simulation schedule
+
+// See /usr/genesis/startup/escapelist.g for macro definitions.  These allow
+// you to use cursor keys for the recall and editing of previous commands
+include          escapelist      // setup macro keys for DEC and SUN keyboards
+"""
+
+
+def install_genesis(get_latest=False):
+    genpath = os.path.join(os.environ["HOME"], "genesis")
+    os.mkdir(genpath)
+    with working_dir(genpath):
+        print(
+            co(
+                [
+                    "wget",
+                    "-nv",
+                    "https://github.com/borismarin/genesis2.4gamma/archive/master.zip",
+                ]
+            )
+        )
+        print(co(["unzip", "master.zip"]))
+        print(co(["ls", "-la", "genesis2.4gamma-master"]))
+        os.chdir("genesis2.4gamma-master/src")
+        print(co(["./configure"]))
+        print(co(["make"]))
+        open(os.path.join(os.environ["HOME"], ".simrc"), "w").write(simrc)

omv/engines/getjlems.py

@@ -0,0 +1,20 @@
+import os
+from subprocess import check_output as co
+
+from omv.common.inout import inform
+from omv.engines.utils.wdir import working_dir
+
+
+def install_jlems():
+    install_root = os.environ["HOME"]
+
+    with working_dir(install_root):
+        print(co(["git", "clone", "https://github.com/LEMS/jLEMS.git"]))
+        inform("Successfully cloned jLEMS", indent=2, verbosity=1)
+
+    path = os.path.join(install_root, "jLEMS")
+
+    with working_dir(path):
+        print(co(["git", "checkout", "development"]))
+        print(co(["mvn", "install"]))
+        inform("Successfully installed jLEMS", indent=2, verbosity=1)

omv/engines/getjnml.py

@@ -0,0 +1,48 @@
+import os
+import platform
+from subprocess import check_output
+from pathlib import Path
+
+from omv.engines.utils.wdir import working_dir
+from omv.common.inout import inform
+
+
+def install_jnml(version):
+
+    if not version:
+        version = "v0.12.4"
+
+    try:
+        jnmlhome = os.environ["JNML_HOME"]
+        jnmlpath = Path(jnmlhome).parent
+    except KeyError:
+        osname = platform.system()
+        if osname == "Linux":
+            try:
+                jnmlpath = os.path.join(os.environ["XDG_DATA_HOME"], "jnml")
+            except KeyError:
+                localsharepath = os.path.join(os.environ["HOME"], ".local/share")
+                if os.path.isdir(localsharepath):
+                    jnmlpath = os.path.join(localsharepath, "jnml")
+                else:
+                    jnmlpath = os.path.join(os.environ["HOME"], "jnml")
+
+        elif osname == "Darwin":
+            jnmlpath = os.path.join(os.environ["HOME"], "Library/jnml")
+        else:
+            jnmlpath = os.path.join(os.environ["HOME"], "jnml")
+
+    if not os.path.isdir(jnmlpath):
+        os.mkdir(jnmlpath)
+    with working_dir(jnmlpath):
+        check_output(
+            [
+                "wget",
+                "-nv",
+                "https://github.com/NeuroML/jNeuroML/releases/download/%s/jNeuroML.zip"
+                % (version),
+            ]
+        )
+        check_output(["unzip", "jNeuroML.zip"])
+
+    inform("Successfully installed jNeuroML "+version, indent=1)

omv/engines/getlibsbml.py

@@ -0,0 +1,13 @@
+from omv.common.inout import pip_install, inform
+
+
+def install_libsbml(version=None):
+    try:
+        pip_install("python-libsbml", version)
+        import libsbml
+
+        m = "Successfully installed libsbml v%s..." % libsbml.__version__
+    except Exception as e:
+        m = "ERROR installing libsbml: " + str(e)
+    finally:
+        inform(m, indent=2)

omv/engines/getmoose.py

@@ -0,0 +1,15 @@
+from omv.common.inout import pip_install
+
+
+def install_moose(version):
+    if not version:
+        version = "4.0.0"
+    try:
+        pip_install("pymoose", version)
+        import moose
+
+        m = "Successfully installed MOOSE..."
+    except Exception as e:
+        m = "ERROR installing MOOSE: " + str(e)
+    finally:
+        print(m)

omv/engines/getnest.py

@@ -0,0 +1,62 @@
+import os
+from omv.common.inout import inform, check_output
+
+from omv.engines.utils.wdir import working_dir
+from sysconfig import get_paths
+import sys
+
+
+def install_nest(version):
+    if not version:
+        version = "3.3"
+
+    inform("Installing NEST", indent=2, verbosity=1)
+    nestpath = os.path.join(os.environ["HOME"], "nest")
+    nestpath2 = os.path.join(os.environ["HOME"], "nest/nest")
+    nestinstallpath = os.path.join(os.environ["HOME"], "nest/nest")
+    if "NEST_INSTALL_DIR" in os.environ:
+        nestinstallpath = os.environ["NEST_INSTALL_DIR"] + "/"
+
+    inform(
+        "Installing NEST (src: %s), (tgt: %s)" % (nestpath, nestinstallpath),
+        indent=2,
+        verbosity=1,
+    )
+    pypaths = get_paths()
+    inform("Python lib info: %s" % (pypaths), indent=2, verbosity=1)
+
+    try:
+        os.mkdir(nestpath)
+    except:
+        pass
+
+    with working_dir(nestpath):
+        # version='2.10.0'
+        check_output(
+            [
+                "wget",
+                "-nv",
+                "https://github.com/nest/nest-simulator/archive/v%s.tar.gz" % (version),
+            ]
+        )
+        check_output(["tar", "xzvf", "v%s.tar.gz" % version])
+        check_output(["mv", "nest-simulator-%s" % version, "nest"], cwd=nestpath)
+
+    with working_dir(nestpath2):
+        check_output(
+            [
+                "cmake",
+                "-DCMAKE_INSTALL_PREFIX:PATH=%s" % nestinstallpath,
+                "-DPYTHON_EXECUTABLE:FILEPATH=%s" % (sys.executable),
+                "-DPYTHON_INCLUDE_DIR=%s" % pypaths["include"],
+                ".",
+            ]
+        )
+        # "-DPYTHON_LIBRARY=%s/libpython3.8m.so" % pypaths['stdlib'],
+        # -DPYTHON_INCLUDE_DIR2=/usr/include/x86_64-linux-gnu/python3.4m"%(nestinstallpath, pypaths['scripts'], pypaths['stdlib'], pypaths['include'], pypaths[''])])
+        check_output(["make", "-j7"])
+        check_output(["make", "install"])
+
+
+if __name__ == "__main__":
+    install_nest()

omv/engines/getnetpyne.py

@@ -0,0 +1,52 @@
+from omv.common.inout import check_output
+from omv.engines.utils.wdir import working_dir
+from omv.common.inout import pip_install
+import os
+import sys
+
+
+def install_netpyne(version=None):
+    if version is not None:
+        pip_install("netpyne", version)
+        import netpyne
+
+    else:
+        install_root = os.environ["HOME"]
+        install_dir = "netpyneInstall"
+        path = os.path.join(install_root, install_dir)
+
+        if not os.path.isdir(path):
+            with working_dir(install_root):
+                print(
+                    check_output(
+                        [
+                            "git",
+                            "clone",
+                            "https://github.com/Neurosim-lab/netpyne.git",
+                            install_dir,
+                        ]
+                    )
+                )
+
+        with working_dir(path):
+            print(check_output(["git", "checkout", "neuroml_updates"]))
+            print(check_output(["pwd"]))
+
+        with working_dir(path):
+            if sys.version_info.major == 2:
+                # pip_install([]'setuptools==42.0.1')
+                pip_install(
+                    [
+                        "kiwisolver==1.0.1",
+                        "matplotlib==2.2.4",
+                        "pandas==0.23.4",
+                        "bokeh==1.4.0",
+                        "Pillow==5.4.1",
+                        "matplotlib-scalebar==0.5.1",
+                        "scipy==1.2.2",
+                        "python-dateutil==2.8.0",
+                    ]
+                )
+            pip_install(".")
+
+        m = "Successfully installed NetPyNE..."

omv/engines/getneuroconstruct.py

@@ -0,0 +1,31 @@
+import os
+from omv.common.inout import inform, check_output as co
+from omv.engines.utils.wdir import working_dir
+
+
+def install_neuroconstruct():
+    try:
+        install_root = os.environ["HOME"]
+
+        with working_dir(install_root):
+            print(
+                co(
+                    [
+                        "git",
+                        "clone",
+                        "https://github.com/NeuralEnsemble/neuroConstruct.git",
+                    ]
+                )
+            )
+
+        path = os.path.join(install_root, "neuroConstruct")
+
+        with working_dir(path):
+            print(co(["./updatenC.sh"]))
+            print(co(["./nC.sh", "-make"]))
+            m = "Successfully installed neuroConstruct..."
+
+    except Exception as e:
+        m = "ERROR installing neuroConstruct: " + str(e)
+    finally:
+        inform(m)

omv/engines/getnml2.py

@@ -0,0 +1,26 @@
+import os
+from subprocess import check_output as co
+
+from omv.common.inout import inform
+from omv.engines.utils.wdir import working_dir
+
+install_root = os.environ["HOME"]
+
+default_nml2_dir = os.path.join(install_root, "NeuroML2")
+
+
+def is_nml2_installed():
+    history_file = os.path.join(default_nml2_dir, "HISTORY.md")
+    if os.path.exists(default_nml2_dir) and os.path.exists(history_file):
+        return True
+    else:
+        return False
+
+
+def install_nml2():
+    with working_dir(install_root):
+        print(co(["git", "clone", "https://github.com/NeuroML/NeuroML2.git"]))
+    with working_dir(default_nml2_dir):
+        print(co(["git", "checkout", "development"]))
+
+    inform("Successfully cloned NeuroML2", indent=2, verbosity=1)

omv/engines/getnrn.py

@@ -0,0 +1,60 @@
+import os
+import sys
+from subprocess import check_output as co
+from distutils.core import run_setup
+from omv.common.inout import inform
+from omv.common.inout import pip_install
+
+from omv.engines.utils.wdir import working_dir
+
+
+def install_neuron(version):
+    if not version:
+        if sys.version_info.major == 3:
+            version = "8.1"  # 8.1 works with pynn 0.10.1
+        else:
+            version = "7.6"
+
+    if sys.version_info.major == 3 and ("7.8" in version or "8." in version):
+        pip_install("neuron==%s" % version)
+        import neuron
+
+        inform("Successfully installed NEURON v%s using pip.." % version, indent=2)
+    else:
+        nrnpath = os.path.join(os.environ["HOME"], "neuron")
+
+        inform("Installing NEURON %s into %s" % (version, nrnpath), indent=1)
+        os.mkdir(nrnpath)
+        with working_dir(nrnpath):
+            nrn_url = (
+                "https://www.neuron.yale.edu/ftp/neuron/versions/v%s/nrn-%s.tar.gz"
+                % (version, version)
+            )
+            dl_file = "nrn-%s.tar.gz" % version
+
+            # See below re 7.8 on py2...
+            if "7.8" in version or "8.0" in version:
+                nrn_url = "https://github.com/neuronsimulator/nrn/archive/%s.tar.gz" % (
+                    version
+                )
+                dl_file = "%s.tar.gz" % version
+            print(co(["wget", "-nv", nrn_url]))
+            print(co(["tar", "xzvf", dl_file]))
+            print(co(["mv", "nrn-%s" % version, "nrn"]))
+            os.chdir("nrn")
+
+            path = os.getcwd()
+            pyexec = sys.executable
+            # Needs to be updated if Neuron >=7.8...
+            co(
+                [
+                    "./configure --prefix=%s --without-iv --with-nrnpython=%s"
+                    % (path, pyexec)
+                ],
+                shell=True,
+            )
+            print(co(["make", "-j3"]))
+            print(co(["make", "install"]))
+
+            os.chdir("src/nrnpython")
+            run_setup("./setup.py", ["install"])

omv/engines/getoctave.py

@@ -0,0 +1,11 @@
+from omv.common.inout import inform, check_output
+
+
+def install_octave():
+    inform("Installing Octave", indent=2, verbosity=1)
+
+    check_output(["apt-get", "install", "octave"])
+
+
+if __name__ == "__main__":
+    install_octave()

omv/engines/getpylems.py

@@ -0,0 +1,13 @@
+from omv.common.inout import pip_install
+
+
+def install_pylems():
+    try:
+        pip_install("pylems")
+        import lems
+
+        m = "Successfully installed pylems v%s..." % lems.__version__
+    except Exception as e:
+        m = "ERROR installing pylems: " + str(e)
+    finally:
+        print(m)

omv/engines/getpyneuroml.py

@@ -0,0 +1,14 @@
+from omv.common.inout import pip_install, inform
+
+
+def install_pynml(version=None):
+    try:
+        pip_install("pyneuroml", version)
+        import neuroml
+        import pyneuroml
+
+        m = "Successfully installed pyNeuroML v%s..." % pyneuroml.__version__
+    except Exception as e:
+        m = "ERROR installing pyNeuroML: " + str(e)
+    finally:
+        inform(m, indent=2)

omv/engines/getpynn.py

@@ -0,0 +1,40 @@
+import os
+from omv.common.inout import inform, check_output
+from omv.common.inout import pip_install
+
+from omv.engines.utils.wdir import working_dir
+
+
+def install_pynn(version=None):
+    if not version:
+        version = "0.10.1"
+
+    try:
+        # pip_install('lazyarray')  # This should ideally be automatically installed with PyNN...
+        # pip_install('neo>=0.11.0')  # This should ideally be automatically installed with PyNN...
+
+        install_root = os.environ["HOME"]
+
+        pyNN_src = "PyNN_src"
+        with working_dir(install_root):
+            check_output(
+                ["git", "clone", "https://github.com/NeuralEnsemble/PyNN.git", pyNN_src]
+            )
+
+        path = os.path.join(install_root, pyNN_src)
+
+        with working_dir(path):
+            print(
+                check_output(["git", "checkout", version])
+            )  # neuroml branch has the latest NML2 import/export code!
+            # check_output(['git','checkout','master'])
+            # print(check_output(['python', 'setup.py', 'install']))
+            pip_install(".")
+            print(check_output(["pwd"]))
+            print("Finished attempting to install PyNN")
+        # import pyNN
+        m = "Successfully installed pyNN..."
+    except Exception as e:
+        m = "ERROR during install_pynn: %s" % e
+    finally:
+        inform(m)

omv/engines/jlems.py

@@ -0,0 +1,48 @@
+import os
+import subprocess as sp
+
+from omv.common.inout import inform, trim_path, check_output, is_verbose
+from omv.engines.engine import OMVEngine, EngineExecutionError
+
+
+class JLemsEngine(OMVEngine):
+    name = "jLEMS"
+
+    @staticmethod
+    def is_installed():
+        ret = True
+        try:
+            ret_str = check_output(["lems", "-h"], verbosity=1)
+            ret = "v%s" % ret_str.split("-jar")[-1].split()[0].split("-")[1][:-4]
+        except OSError as err:
+            if is_verbose():
+                inform("Couldn't execute lems:", err, indent=1)
+            ret = False
+        return ret
+
+    def install(self, version):
+        from omv.engines.getjlems import install_jlems
+
+        home = os.environ["HOME"]
+        p = os.path.join(home, "jLEMS")
+        self.path = p
+        self.environment_vars = {"LEMS_HOME": p}
+        inform("Will fetch and install the latest jLEMS", indent=2)
+        install_jlems()
+        inform("Done...", indent=2)
+
+    def run(self):
+        try:
+            inform("Running file %s with jLEMS" % trim_path(self.modelpath), indent=1)
+            self.stdout = sp.check_output(
+                ["lems", self.modelpath, "-nogui"], cwd=os.path.dirname(self.modelpath)
+            )
+            self.returncode = 0
+        except sp.CalledProcessError as err:
+            self.returncode = err.returncode
+            self.stdout = err.output
+            raise EngineExecutionError
+        except Exception as err:
+            inform("Another error with running jLEMS:", err, indent=1)
+            self.returncode = -1
+            self.stdout = "???"