From 27a4fe1c248347456d111b895e4f88767cc5185e Mon Sep 17 00:00:00 2001 From: Adam Fekete Date: Tue, 19 Jan 2021 19:33:52 +0100 Subject: [PATCH 1/3] loading files directly --- jupyter_jsmol/viewer.py | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/jupyter_jsmol/viewer.py b/jupyter_jsmol/viewer.py index 27ba7ea..e6a703a 100644 --- a/jupyter_jsmol/viewer.py +++ b/jupyter_jsmol/viewer.py @@ -102,7 +102,7 @@ def load(self, filename: str, *args: str, inline: bool = True): # Keeping it only for backwards compatibility. return self.load_file(filename, *args, inline=inline) - def load_file(self, filename: str, *args: str, inline: bool = True): + def load_file(self, filename: str, *args: str, inline: bool = False): if inline: with open(filename, mode='r') as file: @@ -118,7 +118,7 @@ def load_str(self, data: str, *args: str): return self.script(script) @classmethod - def from_file(cls, filename: str, *args: str, inline: bool = True): + def from_file(cls, filename: str, *args: str, inline: bool = False): if inline: with open(filename, mode='r') as file: From cb7025319ba8f1ff3193c7ee6bbb11bbad86ae17 Mon Sep 17 00:00:00 2001 From: Adam Fekete Date: Tue, 19 Jan 2021 19:44:12 +0100 Subject: [PATCH 2/3] clean up the examples --- examples/1 - Basic usage.ipynb | 6 +++--- examples/2 - Advanced scripting.ipynb | 6 +++--- examples/3 - Building an interactive view.ipynb | 6 +++--- 3 files changed, 9 insertions(+), 9 deletions(-) diff --git a/examples/1 - Basic usage.ipynb b/examples/1 - Basic usage.ipynb index 56e5d68..5f9aae0 100644 --- a/examples/1 - Basic usage.ipynb +++ b/examples/1 - Basic usage.ipynb @@ -28,7 +28,7 @@ "cell_type": "markdown", "metadata": {}, "source": [ - "Loading a structure from file (by default this method loads the file \"inline\"): " + "Loading a structure from file (by default this method loads the file directly by using its path): " ] }, { @@ -40,7 +40,7 @@ "outputs": [], "source": [ "view1 = JsmolView.from_file(\"data/c2h410.xyz\") \n", - "# view1 = JsmolView.from_file(\"data/c2h410.xyz\", inline=False) \n", + "# view1 = JsmolView.from_file(\"data/c2h410.xyz\", inline=True) \n", "view1" ] }, @@ -444,7 +444,7 @@ "name": "python", "nbconvert_exporter": "python", "pygments_lexer": "ipython3", - "version": "3.7.6" + "version": "3.8.5" }, "pycharm": { "stem_cell": { diff --git a/examples/2 - Advanced scripting.ipynb b/examples/2 - Advanced scripting.ipynb index 1cd7174..c15331b 100644 --- a/examples/2 - Advanced scripting.ipynb +++ b/examples/2 - Advanced scripting.ipynb @@ -33,7 +33,7 @@ "metadata": {}, "outputs": [], "source": [ - "view1 = JsmolView.from_file(\"data/c2h410.xyz\", inline=False)\n", + "view1 = JsmolView.from_file(\"data/c2h410.xyz\")\n", "view1" ] }, @@ -176,7 +176,7 @@ }, "outputs": [], "source": [ - "view1 = JsmolView.from_file(\"data/c2h410.xyz\", inline=False)\n", + "view1 = JsmolView.from_file(\"data/c2h410.xyz\")\n", "view1" ] }, @@ -459,7 +459,7 @@ "name": "python", "nbconvert_exporter": "python", "pygments_lexer": "ipython3", - "version": "3.7.6" + "version": "3.8.5" } }, "nbformat": 4, diff --git a/examples/3 - Building an interactive view.ipynb b/examples/3 - Building an interactive view.ipynb index 5fc5d82..6d600cc 100644 --- a/examples/3 - Building an interactive view.ipynb +++ b/examples/3 - Building an interactive view.ipynb @@ -89,7 +89,7 @@ "\n", "display(view2)\n", "\n", - "view2.load('data/CO2-DZV-hess.log', inline=False)\n", + "view2.load('data/CO2-DZV-hess.log')\n", "# view2.script('load data/CO2-DZV-hess.log')\n", "view2.script('frame 6; vibration SCALE 1; vibration 1')" ] @@ -107,7 +107,7 @@ "metadata": {}, "outputs": [], "source": [ - "view3 = JsmolView.from_file(\"data/c2h410.xyz\", inline=False)\n", + "view3 = JsmolView.from_file(\"data/c2h410.xyz\")\n", "view3" ] }, @@ -168,7 +168,7 @@ "name": "python", "nbconvert_exporter": "python", "pygments_lexer": "ipython3", - "version": "3.7.6" + "version": "3.8.5" } }, "nbformat": 4, From fa876550517ff690cb2c15169d839c5d1da27d7e Mon Sep 17 00:00:00 2001 From: Adam Fekete Date: Tue, 19 Jan 2021 19:47:27 +0100 Subject: [PATCH 3/3] bumping up the version --- js/package.json | 2 +- jupyter_jsmol/_frontend.py | 2 +- jupyter_jsmol/_version.py | 2 +- setup.py | 2 +- 4 files changed, 4 insertions(+), 4 deletions(-) diff --git a/js/package.json b/js/package.json index 87cac78..170d0ba 100644 --- a/js/package.json +++ b/js/package.json @@ -1,6 +1,6 @@ { "name": "jupyter-jsmol", - "version": "0.2.4", + "version": "0.2.5", "author": { "name": "Adam Fekete", "email": "adam@fekete.co.uk" diff --git a/jupyter_jsmol/_frontend.py b/jupyter_jsmol/_frontend.py index 4bb8e2f..1da7dfd 100644 --- a/jupyter_jsmol/_frontend.py +++ b/jupyter_jsmol/_frontend.py @@ -9,4 +9,4 @@ """ module_name = "jupyter-jsmol" -module_version = "^0.2.4" +module_version = "^0.2.5" diff --git a/jupyter_jsmol/_version.py b/jupyter_jsmol/_version.py index e220fe3..4f0c45a 100644 --- a/jupyter_jsmol/_version.py +++ b/jupyter_jsmol/_version.py @@ -4,5 +4,5 @@ # Copyright (c) Adam Fekete. # Distributed under the terms of the Modified BSD License. -version_info = (0, 2, 4) +version_info = (0, 2, 5) __version__ = ".".join(map(str, version_info)) diff --git a/setup.py b/setup.py index 8151f36..efd4e25 100644 --- a/setup.py +++ b/setup.py @@ -28,7 +28,7 @@ description='JSmol viewer widget for Jupyter', long_description=long_description, long_description_content_type="text/markdown", - version='0.2.4', + version='0.2.5', author='Adam Fekete', author_email='adam@fekete.co.uk', url='https://github.com/fekad/jupyter-jsmol',