dendrotweaks 0.3.1__py3-none-any.whl → 0.4.0__py3-none-any.whl

dendrotweaks/membrane/io/loader.py

@@ -1,90 +0,0 @@
-import os
-import shutil
-import subprocess
-import neuron
-from neuron import h
-
-from pprint import pprint
-
-class MODFileLoader():
-
-    def __init__(self):
-        self._loaded_mechanisms = set()
-        self.verbose = False
-              
-    # LOADING METHODS
-
-    def _get_mechanism_dir(self, path_to_mod_file: str) -> str:
-        """
-        Get the subdirectory for the given mod file.
-
-        Parameters
-        ----------
-        path_to_mod_file : str
-            Path to the .mod file.
-
-        Returns
-        -------
-        str
-            Path to the subdirectory for the mechanism.
-        """
-        mechanism_name = os.path.basename(path_to_mod_file).replace('.mod', '')
-        parent_dir = os.path.dirname(path_to_mod_file)
-        return os.path.join(parent_dir, mechanism_name)
-
-    def load_mechanism(self, path_to_mod_file: str, 
-                       recompile: bool = False) -> None:
-        """
-        Load a mechanism from the specified mod file.
-        Uses the NEURON neuron.load_mechanisms method to make
-        the mechanism available in the hoc interpreter.
-        Creates a temporary directory for the mechanism files
-        to be able to dynamically load mechanisms.
-
-        Parameters
-        ----------
-        path_to_mod_file : str
-            Path to the .mod file.
-        recompile : bool
-            Force recompilation even if already compiled.
-        """
-        mechanism_name = os.path.basename(path_to_mod_file).replace('.mod', '')
-        mechanism_dir = self._get_mechanism_dir(path_to_mod_file)
-        x86_64_dir = os.path.join(mechanism_dir, 'x86_64')
-
-        if self.verbose: print(f"{'=' * 60}\nLoading mechanism {mechanism_name} to NEURON...\n{'=' * 60}")
-
-        if mechanism_name in self._loaded_mechanisms:
-            if self.verbose: print(f'Mechanism "{mechanism_name}" already loaded')
-            return
-
-        if recompile and os.path.exists(mechanism_dir):
-            shutil.rmtree(mechanism_dir)
-
-        if not os.path.exists(x86_64_dir):
-            if self.verbose: print(f'Compiling mechanism "{mechanism_name}"...')
-            os.makedirs(mechanism_dir, exist_ok=True)
-            shutil.copy(path_to_mod_file, mechanism_dir)
-            self._compile_files(mechanism_dir)
-
-        if hasattr(h, mechanism_name):
-            if self.verbose: print(f'Mechanism "{mechanism_name}" already exists in hoc')
-        else:
-            try:
-                neuron.load_mechanisms(mechanism_dir)
-            except Exception as e:
-                print(f"Failed to load mechanism {mechanism_name}: {e}")
-                return
-        self._loaded_mechanisms.add(mechanism_name)
-        if self.verbose: print(f'Loaded mechanism "{mechanism_name}"')
-
-    # HELPER METHODS
-
-    
-    def _compile_files(self, path: str) -> None:
-        """Compile the MOD files in the specified directory."""
-        try:
-            subprocess.run(["nrnivmodl"], cwd=path, check=True)
-        except subprocess.CalledProcessError as e:
-            print(f"Compilation failed: {e}")
-

dendrotweaks-0.3.1.dist-info/RECORD

@@ -1,56 +0,0 @@
-dendrotweaks/__init__.py,sha256=Oty4wVcVFs_9w7L9peCncnzQKFubqkRHyf4c3HKfwWY,385
-dendrotweaks/model.py,sha256=wy17K85d95bD1ioibhDxs8rcNCzow3BP1OVam1b1bTM,67445
-dendrotweaks/model_io.py,sha256=xwXKMcUle-Y0HoWFYVZu3G8v4pdQXmeaDfl2Xi65eHw,2137
-dendrotweaks/path_manager.py,sha256=SfZ7Br-WmUhpvdRTgeOqMzaYVgLpXoSGbekxJvNkZT4,8794
-dendrotweaks/simulators.py,sha256=cVbzbhE48D1ovn7Rg8bU0pI9ztbEqQF2da5gnEMu8Ec,6137
-dendrotweaks/utils.py,sha256=jaUJNb39Bsevg3WJByP56bO7CLj1wzlh-uGZl-lxi1I,7131
-dendrotweaks/analysis/__init__.py,sha256=SEYpoQ5iXiQXyHB20-IAdDHYI-7CR5GYFXIwr-O05Ug,858
-dendrotweaks/analysis/ephys_analysis.py,sha256=oXRjad34tKMDiqEO11uZibHpe2auB2GCetcgd2rVP-o,14124
-dendrotweaks/analysis/morphometric_analysis.py,sha256=5zohjGssyx-wezI-yY3Q-kYM_wzAQLLFBJ9Xk950_JY,3571
-dendrotweaks/membrane/__init__.py,sha256=H3KsbVQonC1BKBnuchAIxGXj5Zl-xN3egOanVUkgs-o,322
-dendrotweaks/membrane/distributions.py,sha256=ADPFPA-CN7AbRJj0Ry4TxFZJhdYXJm87iIGWZSDr5vI,10299
-dendrotweaks/membrane/groups.py,sha256=qN4Q-YodXVLmpGRYvWlZ7Kd9gVnLSK1l4g2Qc0T8dYs,3483
-dendrotweaks/membrane/mechanisms.py,sha256=F4b6VqI3IjyoOQ6GAFvcy7er5-BFCca8JFnQB_HmjmI,18352
-dendrotweaks/membrane/default_mod/AMPA.mod,sha256=HY_pWzYvaSDV-w7qruenG2mnll8v79s40HFHjUCIi4U,980
-dendrotweaks/membrane/default_mod/AMPA_NMDA.mod,sha256=ztv2ePUiEQZ93-23FTkGO2DC91rehQuqo0NUIbHZ368,2318
-dendrotweaks/membrane/default_mod/CaDyn.mod,sha256=gwc69K_rxu2w_mV7CnOSOnVaCMc8Z-MfdBFf6lAj4kg,1298
-dendrotweaks/membrane/default_mod/GABAa.mod,sha256=jdGRid-Wzw4y9kHvq74oSMogLhSiS-Ac2DDaLOrxVi8,983
-dendrotweaks/membrane/default_mod/Leak.mod,sha256=u0lwMYGgl5kNZN5W4N6YHgRSeVxb-z2oM9fqou5rCV8,420
-dendrotweaks/membrane/default_mod/NMDA.mod,sha256=tT4Q5UPoeztXcQ45uZc2PUO3-8OkDLCmrS7WDsn1yQQ,1185
-dendrotweaks/membrane/default_mod/vecstim.mod,sha256=iSpJgR96O2Z3pLNUFIsZ7YJ529ncKUBaZqDJvA0_oV0,965
-dendrotweaks/membrane/default_templates/NEURON_template.py,sha256=BlvA48B48f0AyiepXmrOmGJL5Xe5XDshG9w6h5gDEEs,14874
-dendrotweaks/membrane/default_templates/default.py,sha256=vDxND86RJEw7XHajkg5P0vM2Oss5dyW5m_ugLMeCbT0,2145
-dendrotweaks/membrane/default_templates/standard_channel.mod,sha256=Jpu2rxldAE6kxaylIlPc80F5wpKETodpOvoMbFXhWTA,2861
-dendrotweaks/membrane/default_templates/template_jaxley.py,sha256=t-GsCSUyQ7rDoaLmyuWd9bIxB8W3bCqJdnikD59EVvI,3676
-dendrotweaks/membrane/default_templates/template_jaxley_new.py,sha256=I62KhnOYNV1bT-nPsDTxjIISYmDcso2X8rnsos28nYs,3631
-dendrotweaks/membrane/io/__init__.py,sha256=r84iLBrdmCgGP-dG9iaamBHUGldtAgPyqSujU-3U8ik,584
-dendrotweaks/membrane/io/ast.py,sha256=wnJNy2ga1DsZWQ1lpp1QhK2jvM4aDph7u_27VmyJcXw,5894
-dendrotweaks/membrane/io/code_generators.py,sha256=jhyjvTisV-tavz_yuQ-tOa3JJ56UNUk_pkN9xS6GEqQ,11407
-dendrotweaks/membrane/io/converter.py,sha256=vNCKDk0JqdoqxMWGi2AxT-TZ2YS2itUc7bpm9pRX-6o,3374
-dendrotweaks/membrane/io/factories.py,sha256=rCfZiubZPmikB8nxfjh3Dzg4ZHUXgZX79kmJZDLovwI,4979
-dendrotweaks/membrane/io/grammar.py,sha256=TJLTDlr8Ajp3J9DJ4IvulOCcpUkYr7HnoI0TGnNuEPc,11677
-dendrotweaks/membrane/io/loader.py,sha256=vUh6YMozKD-MvrP2mNyW4-vRoYxXJwK1W4QFUSgcLGU,3042
-dendrotweaks/membrane/io/parser.py,sha256=-SuY9PxlIS5l0bAGuEgLAn89n3F2Ss-X24ehGGZY81o,17921
-dendrotweaks/membrane/io/reader.py,sha256=JWm5WM9illvSfDkhWEmWBcj8Y7PSi8zeZX9j1ARUHVU,6576
-dendrotweaks/morphology/__init__.py,sha256=aqJTQOpRVOYcbWqZ2q4e-Oy735r9_ubW-uE_5cFZVtI,323
-dendrotweaks/morphology/domains.py,sha256=Y4txcGdBdl2aK1DfbTRziNtDyd6bChczwpCWE7lTFzg,2391
-dendrotweaks/morphology/point_trees.py,sha256=5dUPaQXYPdJbWoD3pFI2DV2XnuFRhB5d0wTBlfmmIeI,21600
-dendrotweaks/morphology/sec_trees.py,sha256=FMreuh5mN3oXtvy13oqEc8t-r8a36CPfdkaOqeNo2ts,36894
-dendrotweaks/morphology/seg_trees.py,sha256=uwL1X9qeFNyJVHua1I3rhp0fLSRrS2TAVyb1Fnw4RwQ,3595
-dendrotweaks/morphology/trees.py,sha256=NrNvPMR-U0clt63eqwVJqU0H8NJgY53QGA_BkdcwkQI,16033
-dendrotweaks/morphology/io/__init__.py,sha256=gAZqZdf5VKPb6ksK8Lwt7MbTAq8TDP8uq3Vs_ebNFEY,324
-dendrotweaks/morphology/io/factories.py,sha256=NngNINw73diGK7fud314JzWVhxv2aYLuA9wUuQA0Diw,6344
-dendrotweaks/morphology/io/reader.py,sha256=hW3c541WtG1rNag_YreEhvrLzm8-OTtw0fQREeHDthM,1913
-dendrotweaks/morphology/io/validation.py,sha256=lVkYw9y9yG5QpRh_N0YQ3FbZwuSUsQfSqJTMumMcDdc,7872
-dendrotweaks/morphology/reduce/__init__.py,sha256=p6Mg3KDHxTt8S4DtI0m7L7MqV6dS2pdIYAwB7B-toVw,921
-dendrotweaks/morphology/reduce/reduce.py,sha256=5czZDrG3xsvHn3c_tbYhUOlXgST989-RS-ntbhlvvA0,6361
-dendrotweaks/morphology/reduce/reduced_cylinder.py,sha256=jGJ4J-amukRr-3DPirVR5pzNO-6H7_sZF1N_X57ZGdw,5132
-dendrotweaks/stimuli/__init__.py,sha256=bFfSEZhCVpwOVEBgLe65iiY3SdpjKPhyLemC1z5OX9I,153
-dendrotweaks/stimuli/iclamps.py,sha256=NjkhhwZKJR1f_g3N9BVxMVoO9ubBk5WkQ6h9Bnf9xgA,1681
-dendrotweaks/stimuli/populations.py,sha256=wZwy3PC1uRmQa-WnTLZLy7PGKCQrRJgmmhRIaGdJlLU,7991
-dendrotweaks/stimuli/synapses.py,sha256=g4MgWTske2TZ2i9FIIOE8-KXNx_3dWa3zEhB2rcqYig,5470
-dendrotweaks-0.3.1.dist-info/licenses/LICENSE,sha256=OXLcl0T2SZ8Pmy2_dmlvKuetivmyPd5m1q-Gyd-zaYY,35149
-dendrotweaks-0.3.1.dist-info/METADATA,sha256=jcnz3Eq3NdoALKHhwoE8lnrA5iSNAcO6oPBU3yZ0GJs,2687
-dendrotweaks-0.3.1.dist-info/WHEEL,sha256=1tXe9gY0PYatrMPMDd6jXqjfpz_B-Wqm32CPfRC58XU,91
-dendrotweaks-0.3.1.dist-info/top_level.txt,sha256=OzT_2BSI5j5zxC447K6Y-0W-GHbued7iX-_hFGAKMxY,13
-dendrotweaks-0.3.1.dist-info/RECORD,,