From 917b2a560e4cf6af33653125a0571a4bce614eb6 Mon Sep 17 00:00:00 2001 From: Aaron Virshup Date: Thu, 24 Aug 2017 17:36:31 -0700 Subject: [PATCH 01/24] Version check fixes --- nbmolviz/__main__.py | 2 +- nbmolviz/widget_utils.py | 27 +++++++++++++++++---------- 2 files changed, 18 insertions(+), 11 deletions(-) diff --git a/nbmolviz/__main__.py b/nbmolviz/__main__.py index 50bb547..08d416e 100644 --- a/nbmolviz/__main__.py +++ b/nbmolviz/__main__.py @@ -51,7 +51,7 @@ def main(): if args.command == 'check': print('Expected version:', _version.get_versions()['version']) - versions = install.get_installed_versions('nbmolviz-js', True) + versions = install.get_installed_versions('nbmolviz', True) foundone = False for key, vers in versions.items(): if vers.installed: diff --git a/nbmolviz/widget_utils.py b/nbmolviz/widget_utils.py index 210a311..b80cae6 100644 --- a/nbmolviz/widget_utils.py +++ b/nbmolviz/widget_utils.py @@ -69,6 +69,8 @@ def extensions_install_check(): def print_extension_warnings(stream=sys.stdout): + import pkg_resources + from moldesign import widgets as mdtwidgets from . import install from . import __version__ as nbv_version @@ -86,17 +88,22 @@ def print_extension_warnings(stream=sys.stdout): if not enabled: if installed: - flag = install.FLAGS[installed] warnings.append('- the "{dep}" notebook extension is not enabled. ') - else: - flag = install.FLAGS[preferred_loc] - - if (dep == 'nbmolviz' and enabled and installed): - installed_version = state[dep]['version'] - if installed_version != nbv_version: - warnings.append('- NBMolViz notebook extensions are out of date (extensions are' - ' version %s, but nbmolviz expected %s)' % - (installed_version, nbv_version)) + + if dep == 'nbmolviz': + expected_py_version = pkg_resources.parse_version(mdtwidgets.NBMOLVIZ_EXPECTED_VERSION) + installed_py_version = pkg_resources.parse_version(nbv_version) + if expected_py_version != installed_py_version: + warnings.append( + '- MDT expected nbmolviz version "%s" but version "%s" is installed' % + (expected_py_version, installed_py_version)) + + if enabled and installed: + installed_ext_version = state[dep]['version'] + if installed_ext_version != nbv_version: + warnings.append('- NBMolViz notebook extensions are out of date (extensions are' + ' version %s, but nbmolviz expected %s)' % + (installed_ext_version, nbv_version)) if warnings: print('WARNING: notebook visualizations may not function correctly because:', From f716b0be0952743c5d5c75263e3ffb847e0a8496 Mon Sep 17 00:00:00 2001 From: Aaron Virshup Date: Thu, 24 Aug 2017 17:37:10 -0700 Subject: [PATCH 02/24] Update to latest `ipywidgets` and fix styling changes --- nbmolviz/mdtconfig/docker.py | 16 ++++++++-------- nbmolviz/mdtconfig/images.py | 3 ++- nbmolviz/uielements/logwidget.py | 1 - requirements.txt | 2 +- 4 files changed, 11 insertions(+), 11 deletions(-) diff --git a/nbmolviz/mdtconfig/docker.py b/nbmolviz/mdtconfig/docker.py index 190c2df..7352ec4 100644 --- a/nbmolviz/mdtconfig/docker.py +++ b/nbmolviz/mdtconfig/docker.py @@ -23,18 +23,18 @@ from .images import DockerImageStatus -SPINNER = '
' -CONNECTED = 'connected' -DISCONNECTED = 'disconnected' +SPINNER = 'Engine status:
' +CONNECTED = 'Engine status: connected' +DISCONNECTED = 'Engine status: disconnected' + class DockerConfig(VBox): def __init__(self): self.client = None - self.warning = ipy.HTML(description='Engine status:', value=SPINNER) - self.devmode_label = ipy.Label('Use local docker images (developer mode)', - layout=ipy.Layout(width='100%')) + self.warning = ipy.HTML(value=SPINNER) self.devmode_button = ipy.Checkbox(value=mdt.compute.config.devmode, - layout=ipy.Layout(width='15px')) + description="Use local docker images (developer mode)", + layout=ipy.Layout(width='100%')) self.devmode_button.observe(self.set_devmode, 'value') self.engine_config_description = ipy.HTML('Docker host with protocol and port' @@ -64,7 +64,7 @@ def __init__(self): HBox([self._reset_config_button, self._apply_changes_button, self._save_changes_button]), - HBox([self.devmode_button, self.devmode_label]), + self.devmode_button, self.image_box] self.reset_config() super().__init__(children=self.children) diff --git a/nbmolviz/mdtconfig/images.py b/nbmolviz/mdtconfig/images.py index 67022ce..8428c6b 100644 --- a/nbmolviz/mdtconfig/images.py +++ b/nbmolviz/mdtconfig/images.py @@ -54,8 +54,9 @@ def __init__(self, image, client): self.status = ipy.HTML(layout=ipy.Layout(width="20px")) self.html = ipy.HTML(value=image, layout=ipy.Layout(width="400px")) self.html.add_class('nbv-monospace') + self.html.add_class('nbv-table-row') self.msg = ipy.HTML(layout=ipy.Layout(width='300px')) - self.button = ipy.Button(layout=ipy.Layout(width='100px')) + self.button = ipy.Button(layout=ipy.Layout(width='150px')) if mdt.compute.config.devmode: self.button.on_click(self.rebuild) else: diff --git a/nbmolviz/uielements/logwidget.py b/nbmolviz/uielements/logwidget.py index 7d203c1..addeac9 100644 --- a/nbmolviz/uielements/logwidget.py +++ b/nbmolviz/uielements/logwidget.py @@ -132,7 +132,6 @@ def __init__(self, objects, display=False, **kwargs): self.objs = OrderedDict(objects) super(LoggingTabs, self).__init__(list(objects.values()), **wu.process_widget_kwargs(kwargs)) - self.selected_index = -1 for ikey, key in enumerate(objects.keys()): self.set_title(ikey, key) self._displayed = False diff --git a/requirements.txt b/requirements.txt index 69b81fc..a7c0e14 100644 --- a/requirements.txt +++ b/requirements.txt @@ -1,5 +1,5 @@ future -ipywidgets >= 6.0 +ipywidgets >= 7.0 ipython >= 5.0 moldesign >= 0.8rc1 notebook >= 4.2 From 842369d7f9840d9114aeb8d235209c819cb55e18 Mon Sep 17 00:00:00 2001 From: Aaron Virshup Date: Sun, 27 Aug 2017 22:56:31 -0700 Subject: [PATCH 03/24] Clean up configurators --- nbmolviz/uielements/components.py | 10 ++++++++-- nbmolviz/uielements/configurator.py | 11 +++++++---- nbmolviz/widgets/parameterization.py | 3 ++- 3 files changed, 17 insertions(+), 7 deletions(-) diff --git a/nbmolviz/uielements/components.py b/nbmolviz/uielements/components.py index 17a1049..8d90010 100644 --- a/nbmolviz/uielements/components.py +++ b/nbmolviz/uielements/components.py @@ -85,10 +85,14 @@ class UnitText(ipy.Box): VALID = u"\u2705" def __init__(self, value=None, units=None, **kwargs): + from moldesign import units as u + kwargs.setdefault('display', 'flex') kwargs.setdefault('flex_flow','row wrap') - super().__init__(layout=ipy.Layout(display='flex', flex_flow='row wrap'), - **process_widget_kwargs(kwargs)) + layout = kwargs.pop('layout', ipy.Layout()) + layout.display = 'flex' + layout.flex_flow = 'row wrap' + super().__init__(layout=layout, **kwargs) self.textbox = ipy.Text() self.textbox.observe(self._validate, 'value') self._error_msg = None @@ -106,6 +110,8 @@ def __init__(self, value=None, units=None, **kwargs): self.value = value def _validate(self, change): + from moldesign import units as u + import pint self._validated_value = None diff --git a/nbmolviz/uielements/configurator.py b/nbmolviz/uielements/configurator.py index f26cffa..f9fbdd1 100644 --- a/nbmolviz/uielements/configurator.py +++ b/nbmolviz/uielements/configurator.py @@ -55,19 +55,22 @@ def __init__(self, paramlist, paramdefs, title=None): layout=ipy.Layout(align_self='center')) self.selectors = collections.OrderedDict([(p.name, ParamSelector(p)) for p in paramdefs]) + for v in self.selectors.values(): + v.add_class('nbv-table-row') self.reset_values() title = utils.if_not_none(title, 'Configuration') self.title = ipy.HTML('

%s

' % title, align_self='center') - self.currentconfig = ipy.Textarea(description='Current params', - disabled=True, + self.currentlabel = ipy.Label('Current parameter values:') + self.currentconfig = ipy.Textarea(disabled=True, value=self._pretty_print_config(), layout=ipy.Layout(width='350px', min_height='300px', max_height='500px', display='flex', flex_flow='column')) - self.middle = HBox([VBox(list(self.selectors.values())), self.currentconfig]) + self.middle = HBox([VBox(list(self.selectors.values())), + VBox([self.currentlabel, self.currentconfig])]) self.children = [self.title, self.middle, self.buttons] def reset_values(self, *args): @@ -123,7 +126,7 @@ def __init__(self, paramdef): if paramdef.choices: self.selector = ipy.Dropdown(options=paramdef.choices, **self.WIDGETKWARGS) elif paramdef.type == bool: - self.selector = ipy.ToggleButtons(options=[True, False], **self.WIDGETKWARGS) + self.selector = ipy.Checkbox(**self.WIDGETKWARGS) elif paramdef.units: self.selector = UnitText(units=paramdef.units, **self.WIDGETKWARGS) elif paramdef.type == float: diff --git a/nbmolviz/widgets/parameterization.py b/nbmolviz/widgets/parameterization.py index 1af7ff2..771d540 100644 --- a/nbmolviz/widgets/parameterization.py +++ b/nbmolviz/widgets/parameterization.py @@ -58,7 +58,8 @@ def __init__(self, errormessages, molin, molout=None): self.switch_display({'old': self.errorlist.value, 'new': self.errorlist.value}) self.errorlist.observe(self.switch_display, 'value') children = (self.status, - HBox([self.viewer, VBox([self.listdesc, self.errorlist])]), + self.viewer, + VBox([self.listdesc, self.errorlist]), self.errmsg) super().__init__(children=children, layout=ipy.Layout(display='flex', flex_flow='column')) From f8c1c2b8430c221944df03f5a0a112be223545e0 Mon Sep 17 00:00:00 2001 From: Aaron Virshup Date: Sun, 27 Aug 2017 22:57:34 -0700 Subject: [PATCH 04/24] Clean up install, disable Jupyter data rate limiter --- nbmolviz/install.py | 106 ++++++++++++++++++++++++++++++++++---------- 1 file changed, 82 insertions(+), 24 deletions(-) diff --git a/nbmolviz/install.py b/nbmolviz/install.py index 56ffe58..70deb2f 100644 --- a/nbmolviz/install.py +++ b/nbmolviz/install.py @@ -57,10 +57,16 @@ def location_writable(): config_paths = jupyter_config_dirs() ext_paths = nbextension_ordered_paths() writable = {} - for location in ext_paths: - writable[location] = ( - os.access(config_paths[location], os.W_OK | os.X_OK) and - os.access(ext_paths[location], os.W_OK | os.X_OK)) + for pathname in ext_paths: + confpath = config_paths[pathname] + extpath = ext_paths[pathname] + + confpath = confpath if os.path.exists(confpath) else os.path.dirname(confpath) + extpath = extpath if os.path.exists(extpath) else os.path.dirname(extpath) + + writable[pathname] = ( + os.access(confpath, os.W_OK | os.X_OK) and + os.access(extpath, os.W_OK | os.X_OK)) return writable @@ -75,13 +81,19 @@ def preferred_install_location(): def autoinstall(): - """ Attempt to install and activate the notebook extensions + """ Attempt to install and activate the notebook extensions. + + If a given extension is already installed, this will install the latest version into the + same location. + + Otherwise, it will install into the first writable location in the following list: + 1. virtual environment extensions directory + 2. current user's extensions directory + 3. global extensions directory Raises: ValueError: if there are no writable install locations """ - from moldesign import compute - from . import __version__ as nbv_version from . import widget_utils as wu preferred = preferred_install_location() @@ -90,23 +102,10 @@ def autoinstall(): state = wu.extensions_install_check() for dep in state: - do_install = False - if not state[dep]['installed'] or state[dep]['enabled'] != state[dep]['installed']: - print("Activating '%s' extensions:" % dep) - do_install = True - elif (dep == 'nbmolviz' and - not compute.config.get('skip_nbmolviz_version_check', False) and - state[dep]['installed'] and - state[dep]['version'] != nbv_version): - print("Updating 'nbmolviz' extensions from %s to %s:" % (state[dep]['version'], - nbv_version)) - do_install = True - else: - print("'%s' extensions already activated." % dep) - - if do_install: - activate_extension(dep, FLAGS[preferred]) - + install_location = state[dep]['installed'] if state[dep]['installed'] else preferred + activate_extension(dep, FLAGS[install_location]) + print() + lift_iopub_rate_limit() def get_installed_versions(pyname, getversion): @@ -160,6 +159,65 @@ def get_installed_versions(pyname, getversion): writable[k]) for k in installed} +IOPUB_LINES = """### MOLDESIGN modification +c.NotebookApp.iopub_data_rate_limit = 100000000000 +### END MOLDESIGN MODIFICATION +""" + + +def lift_iopub_rate_limit(): + import textwrap + from jupyter_core import paths as jupypaths + config_dir = jupypaths.jupyter_config_dir() + nbcfgfile = os.path.join(config_dir, 'jupyter_notebook_config.py') + backup_basepath = nbcfgfile+'.bak' + bakfile = backup_basepath + + print("Disabling Jupyter rate limits to allow visualization " + "(see https://github.com/jupyter/notebook/issues/2287 )") + + if not os.path.exists(nbcfgfile): + print("Creating jupyter config file at %s" % nbcfgfile) + cmd = "jupyter notebook --generate-config" + print(" > %s" % cmd) + subprocess.check_call(cmd) + else: + for i in range(100): + # if "jupyter_notebook_config.py.bak.N" exists for N=0...99, we'll overwrite # 99 + # Feel free to submit a PR if you're not OK with this :) + if os.path.exists(bakfile): + bakfile = backup_basepath+('.%d' % i) + else: + break + print('Previous configuration file saved to %s' % bakfile) + + os.rename(nbcfgfile, bakfile) + + print('Adding these lines to the bottom of %s:' % nbcfgfile) + print(textwrap.indent(IOPUB_LINES, ' > '), end='') + + with open(bakfile, 'r') as bakstream, open(nbcfgfile, 'w') as modstream: + found = False + lineiter = iter(bakstream) + while True: + try: + line = next(lineiter) + except StopIteration: + break + + if line.strip() == "### MOLDESIGN modification": + found = True + modstream.write(IOPUB_LINES) + for i in range(2): # remove the next two lines + next(lineiter) + else: + modstream.write(line) + + if not found: + modstream.write(IOPUB_LINES) + + print('These changes will take effect the next time the Jupyter server is started.') + def activate(flags): try: From 4b236a29321bb636da8a2438a0f8924aeb84972e Mon Sep 17 00:00:00 2001 From: Aaron Virshup Date: Sun, 27 Aug 2017 22:58:06 -0700 Subject: [PATCH 05/24] Better orbital animation behavior --- nbmolviz/viewers/orbital_viewer.py | 98 ++++++++++++++------------- nbmolviz/viewers/trajectory_viewer.py | 79 +++++++++++++++++---- 2 files changed, 116 insertions(+), 61 deletions(-) diff --git a/nbmolviz/viewers/orbital_viewer.py b/nbmolviz/viewers/orbital_viewer.py index 3a20aab..442f08a 100644 --- a/nbmolviz/viewers/orbital_viewer.py +++ b/nbmolviz/viewers/orbital_viewer.py @@ -27,8 +27,7 @@ from moldesign import units as u from moldesign.mathutils import padded_grid -from ..viewers import GeometryViewer, translate_color -from ..widget_utils import process_widget_kwargs +from ..viewers import GeometryViewer from ..uielements.components import HBox, VBox from . import ViewerContainer @@ -43,7 +42,7 @@ class OrbitalViewer(ViewerContainer): display (bool): immediately draw the viewer in the notebook **kwargs (dict): kwargs for the viewer """ - current_orbital = traitlets.Any() # reference to the currently displayed orbital + current_orbital = traitlets.Tuple(allow_none=True) isoval = traitlets.Float(0.01) orb_opacity = traitlets.Float(0.8) negative_color = traitlets.Union([traitlets.Integer(), traitlets.Unicode()], default='red') @@ -55,7 +54,8 @@ def __init__(self, mol, display=False, **kwargs): self.orblist = None self.isoval_selector = None self.opacity_selector = None - self.viewer = GeometryViewer(mol=mol, **process_widget_kwargs(kwargs)) + kwargs.setdefault('width', '600px') + self.viewer = GeometryViewer(mol=mol, **kwargs) self.mol = mol self.wfn = mol.wfn # cache this directly because the molecule's state may change self._restyle_orbital() # sets defaults for orbital spec @@ -67,27 +67,21 @@ def __init__(self, mol, display=False, **kwargs): if display: display_now(self) - def draw_orbital(self, orbital): - """Display a molecular orbital - - Args: - orbital (moldesign.orbitals.Orbital): orbital to draw - """ - # This triggers self._redraw_orbital - self.current_orbital = orbital - @traitlets.observe('current_orbital', 'numpoints') def _redraw_orbital(self, *args): + if self.current_orbital is None: + self.viewer.cubefile = '' + return + self.status_element.value = '
' try: - if self.current_orbital is None: - self.viewer.cubefile = '' - return - - orbkey = (id(self.current_orbital), self.numpoints) + orbtype, orbindex = self.current_orbital + orbital = self.wfn.orbitals[orbtype][orbindex] + # Hash orbitals by object ID to support trajectories (where a given orbital may change) + orbkey = (id(orbital), self.numpoints) if orbkey not in self._cached_cubefiles: - grid, values = self._calc_orb_grid(self.current_orbital) + grid, values = self._calc_orb_grid(orbital) cubefile = self._grid_to_cube(grid, values) self._cached_cubefiles[orbkey] = cubefile else: @@ -99,7 +93,6 @@ def _redraw_orbital(self, *args): else: self.status_element.value = '' - @traitlets.observe('negative_color', 'positive_color', 'isoval', @@ -231,12 +224,12 @@ def _make_ui_pane(self, hostheight): traitlets.directional_link((self, 'numpoints'), (self.orb_resolution, 'value'), transform=str) - self.uipane = ipy.VBox([self.status_element, - orbtype_label, self.type_dropdown, - orblist_label, self.orblist, - isoval_label, self.isoval_selector, - opacity_label, self.opacity_selector, - resolution_label, self.orb_resolution, self.resolution_button]) + self.uipane = VBox([self.status_element, + orbtype_label, self.type_dropdown, + orblist_label, self.orblist, + isoval_label, self.isoval_selector, + opacity_label, self.opacity_selector, + resolution_label, self.orb_resolution, self.resolution_button]) self.new_orb_type() self.type_dropdown.observe(self.new_orb_type, 'value') return self.uipane @@ -248,27 +241,40 @@ def new_orb_type(self, *args): newtype = self.type_dropdown.value neworbs = wfn.orbitals[newtype] orblist = collections.OrderedDict() - - orblist[None] = None - for i, orb in enumerate(neworbs): - if hasattr(orb, 'unicode_name'): - orbname = orb.unicode_name - else: - orbname = orb.name - - meta = '' - if orb.energy is not None: - meta = '{:.02fP}'.format(orb.energy.defunits()) - if orb.occupation is not None: - if meta: meta += ', ' - meta += 'occ %.2f' % orb.occupation - if meta: - desc = '%d. %s (%s)' % (i, orbname, meta) + prev_val = self.orblist.value + found_prev_value = False + + with self.hold_trait_notifications(): + orblist[None] = None + for i, orb in enumerate(neworbs): + if hasattr(orb, 'unicode_name'): + orbname = orb.unicode_name + else: + orbname = orb.name + + meta = '' + if orb.energy is not None: + meta = '{:.02fP}'.format(orb.energy.defunits()) + if orb.occupation is not None: + if meta: + meta += ', ' + meta += 'occ %.2f' % orb.occupation + if meta: + desc = '%d. %s (%s)' % (i, orbname, meta) + else: + desc = '%d. %s' % (i, orbname) + + orbkey = (self.type_dropdown.value, orb.index) + orblist[desc] = orbkey + if prev_val == orbkey: + found_prev_value = True + + self.orblist.options = orblist + if found_prev_value: + self.orblist.value = prev_val else: - desc = '%d. %s' % (i, orbname) - orblist[desc] = orb - self.orblist.value = None - self.orblist.options = orblist + self.orblist.value = None + self._redraw_orbital() def change_resolution(self, *args): self.numpoints = int(self.orb_resolution.value) diff --git a/nbmolviz/viewers/trajectory_viewer.py b/nbmolviz/viewers/trajectory_viewer.py index 962ee6c..b2589a3 100644 --- a/nbmolviz/viewers/trajectory_viewer.py +++ b/nbmolviz/viewers/trajectory_viewer.py @@ -15,7 +15,6 @@ # WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. # See the License for the specific language governing permissions and # limitations under the License. - import ipywidgets as ipy import traitlets @@ -40,6 +39,7 @@ class TrajectoryViewer(ViewerContainer): def __init__(self, trajectory, display=False, **kwargs): from IPython.display import display as displaynow + self.playbar = None self.playbutton = None self.slider = None self.viewer = None @@ -89,8 +89,8 @@ def make_controls(self): traitlets.link((self.playbutton, 'value'), (self.slider, 'value')) traitlets.link((self.slider, 'value'), (self, 'current_frame')) - return VBox((self.annotation, - HBox((self.playbutton, self.slider, self.readout)))) + self.playbar = HBox((self.playbutton, self.slider, self.readout)) + return VBox((self.annotation, self.playbar)) @traitlets.observe('current_frame') def _change_frame(self, change): @@ -104,29 +104,78 @@ def __getattr__(self, item): class TrajectoryOrbViewer(TrajectoryViewer): - def _get_viewer_container(self): - orbviewer = self.traj._tempmol.draw_orbitals() - self.viewer = orbviewer.viewer - return orbviewer + def __init__(self, *args, **kwargs): + super().__init__(*args, **kwargs) + self._caching = False + self.cache_orbital_button = ipy.Button() + self.cache_orbital_button.on_click(self.cache_orbitals) + self.viewcontainer.observe(self.handle_orb_update, 'current_orbital') + self.pane.children += (self.cache_orbital_button,) + self.handle_orb_update({'new':None}) def show_frame(self, framenum): wfn = self.traj.frames[framenum].wfn - oldorbital = self.current_orbital - if oldorbital: - orbtype = self.viewcontainer.type_dropdown.value - neworb = wfn.orbitals[orbtype][oldorbital.index] - self.viewcontainer.wfn = wfn with self.hold_trait_notifications(), \ + self.viewcontainer.orblist.hold_sync(), \ self.viewcontainer.hold_trait_notifications(), \ self.viewcontainer.viewer.hold_trait_notifications(), \ - self.viewcontainer.orblist.hold_trait_notifications(): + self.viewcontainer.viewer.hold_sync(): super().show_frame(framenum) self.viewcontainer.new_orb_type() - if oldorbital: - self.orblist.value = neworb + + def cache_orbitals(self, *args): + import threading + self.cache_orbital_button.disabled = True + self._caching = True + threading.Thread(target=self._cache_orbital_thread).start() + + def _cache_orbital_thread(self): + try: + self.cache_orbital_button.button_style = 'info' + self.enable_controls(False) + for fnum in range(self.traj.num_frames): + self.cache_orbital_button.description = 'Calculating frame %d' % fnum + self.show_frame(fnum) + except Exception: + self.cache_orbital_button.description = 'Orbital calc failed' + self.cache_orbital_button.button_style = 'warning' + self.cache_orbital_button.disabled = False + raise + else: + self.cache_orbital_button.description = 'Animation ready.' + self.cache_orbital_button.button_style = 'success' + self.cache_orbital_button.disabled = True + finally: + self.enable_controls(True) + self._caching = False + + def handle_orb_update(self, change): + if self._caching: + return + if change['new'] is None: + self.cache_orbital_button.description = '--' + self.cache_orbital_button.button_style = '' + self.cache_orbital_button.disabled = True + self.playbutton.interval = 100 + elif change['old'] != change['new']: + self.cache_orbital_button.description = 'Prep animation' + self.cache_orbital_button.button_style = 'primary' + self.cache_orbital_button.disabled = False + self.playbutton.interval = 500 + + def enable_controls(self, enabled): + self.viewcontainer.orblist.disabled = not enabled + self.viewcontainer.type_dropdown.disabled = not enabled + self.slider.disabled = not enabled + self.playbutton.disabled = not enabled + + def _get_viewer_container(self): + orbviewer = self.traj._tempmol.draw_orbitals() + self.viewer = orbviewer.viewer + return orbviewer class FrameInspector(ipy.HTML): From 1c44ba192c2b881aab8a3d4627ce65e1c19cfb5f Mon Sep 17 00:00:00 2001 From: Aaron Virshup Date: Wed, 6 Sep 2017 15:16:26 -0700 Subject: [PATCH 06/24] More explicit futurization for py2 compatibility --- nbmolviz/install.py | 13 ++++++++----- nbmolviz/utils.py | 14 ++++++-------- nbmolviz/widget_utils.py | 7 +++---- 3 files changed, 17 insertions(+), 17 deletions(-) diff --git a/nbmolviz/install.py b/nbmolviz/install.py index 70deb2f..fc58d94 100644 --- a/nbmolviz/install.py +++ b/nbmolviz/install.py @@ -1,3 +1,7 @@ +from __future__ import print_function, absolute_import, division +from future.builtins import * +from future import standard_library +standard_library.install_aliases() # Copyright 2017 Autodesk Inc. # # Licensed under the Apache License, Version 2.0 (the "License"); @@ -180,7 +184,7 @@ def lift_iopub_rate_limit(): print("Creating jupyter config file at %s" % nbcfgfile) cmd = "jupyter notebook --generate-config" print(" > %s" % cmd) - subprocess.check_call(cmd) + subprocess.check_call(cmd.split()) else: for i in range(100): # if "jupyter_notebook_config.py.bak.N" exists for N=0...99, we'll overwrite # 99 @@ -193,9 +197,6 @@ def lift_iopub_rate_limit(): os.rename(nbcfgfile, bakfile) - print('Adding these lines to the bottom of %s:' % nbcfgfile) - print(textwrap.indent(IOPUB_LINES, ' > '), end='') - with open(bakfile, 'r') as bakstream, open(nbcfgfile, 'w') as modstream: found = False lineiter = iter(bakstream) @@ -216,7 +217,9 @@ def lift_iopub_rate_limit(): if not found: modstream.write(IOPUB_LINES) - print('These changes will take effect the next time the Jupyter server is started.') + print('The following lines lines were added to the bottom of %s:' % nbcfgfile) + print(textwrap.indent(IOPUB_LINES, ' > '), end='') + print("\nThese changes will take effect the next time Jupyter is launched.") def activate(flags): diff --git a/nbmolviz/utils.py b/nbmolviz/utils.py index 1f48f76..062b660 100644 --- a/nbmolviz/utils.py +++ b/nbmolviz/utils.py @@ -1,4 +1,7 @@ -from __future__ import division +from __future__ import print_function, absolute_import, division +from future.builtins import * +from future import standard_library +standard_library.install_aliases() # Copyright 2017 Autodesk Inc. # # Licensed under the Apache License, Version 2.0 (the "License"); @@ -12,13 +15,8 @@ # WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. # See the License for the specific language governing permissions and # limitations under the License. -from builtins import zip -from builtins import str from past.builtins import basestring -from past.utils import old_div -from builtins import object import uuid - import webcolors @@ -126,8 +124,8 @@ def __mul__(self,other): __rmul__ = __mul__ def __div__(self,other): - newnumber = int( old_div(float(self.number), other)) - return Measure( '%d%s'%(newnumber,self.unit)) + newnumber = int(float(self.number) / other) + return Measure('%d%s'%(newnumber,self.unit)) BENZENE_SDF = """241 diff --git a/nbmolviz/widget_utils.py b/nbmolviz/widget_utils.py index b80cae6..866faa5 100644 --- a/nbmolviz/widget_utils.py +++ b/nbmolviz/widget_utils.py @@ -1,8 +1,7 @@ # -*- coding: utf-8 -*- from __future__ import print_function, absolute_import, division - +from future.builtins import * from future import standard_library - standard_library.install_aliases() # Copyright 2017 Autodesk Inc. # @@ -70,7 +69,7 @@ def extensions_install_check(): def print_extension_warnings(stream=sys.stdout): import pkg_resources - from moldesign import widgets as mdtwidgets + from moldesign import _NBMOLVIZ_EXPECTED_VERSION from . import install from . import __version__ as nbv_version @@ -91,7 +90,7 @@ def print_extension_warnings(stream=sys.stdout): warnings.append('- the "{dep}" notebook extension is not enabled. ') if dep == 'nbmolviz': - expected_py_version = pkg_resources.parse_version(mdtwidgets.NBMOLVIZ_EXPECTED_VERSION) + expected_py_version = pkg_resources.parse_version(_NBMOLVIZ_EXPECTED_VERSION) installed_py_version = pkg_resources.parse_version(nbv_version) if expected_py_version != installed_py_version: warnings.append( From 58eecb7c1a86a7e9365b71273a1b77ecd2c687de Mon Sep 17 00:00:00 2001 From: Aaron Virshup Date: Wed, 6 Sep 2017 15:17:43 -0700 Subject: [PATCH 07/24] Styling tweaks --- nbmolviz/uielements/configurator.py | 2 +- nbmolviz/viewers/geometry_viewer.py | 4 +--- 2 files changed, 2 insertions(+), 4 deletions(-) diff --git a/nbmolviz/uielements/configurator.py b/nbmolviz/uielements/configurator.py index f9fbdd1..a7bbf66 100644 --- a/nbmolviz/uielements/configurator.py +++ b/nbmolviz/uielements/configurator.py @@ -46,7 +46,7 @@ def __init__(self, paramlist, paramdefs, title=None): self.paramlist = paramlist self.paramdefs = paramdefs - self.apply_button = ipy.Button(description='Apply') + self.apply_button = ipy.Button(description='Apply', button_style='primary') self.apply_button.on_click(self.apply_values) self.reset_button = ipy.Button(description='Reset') diff --git a/nbmolviz/viewers/geometry_viewer.py b/nbmolviz/viewers/geometry_viewer.py index 0db96b0..1ed913e 100644 --- a/nbmolviz/viewers/geometry_viewer.py +++ b/nbmolviz/viewers/geometry_viewer.py @@ -161,9 +161,7 @@ def autostyle(self): cartoon_atoms.extend(residue.atoms) elif residue.type in ('water', 'solvent'): line_atoms.extend(residue.atoms) - elif residue.type in ('dna', 'rna') and self.mol.num_atoms > 1000: - cartoon_atoms.extend(residue.atoms) - else: # includes DNA, RNA if molecule is small enough + else: # includes DNA, RNA - ribbon representation currently doesn't work for these stick_atoms.extend(residue.atoms) if cartoon_atoms: From 18177c59ffd12152e7748a7dcb130732c437cf12 Mon Sep 17 00:00:00 2001 From: Aaron Virshup Date: Thu, 7 Sep 2017 00:56:24 -0700 Subject: [PATCH 08/24] Python 2 unicode handling --- NOTICE => NOTICES | 3 +++ nbmolviz/install.py | 9 +++++---- nbmolviz/mdtconfig/compute.py | 2 +- nbmolviz/mdtconfig/docker.py | 2 +- nbmolviz/mdtconfig/images.py | 2 +- nbmolviz/mdtconfig/interfaces.py | 3 ++- nbmolviz/mdtconfig/visualization.py | 2 +- nbmolviz/uielements/configurator.py | 9 +++++++-- nbmolviz/utils.py | 19 +++++++++++++++++++ nbmolviz/viewers/graph_viewer.py | 28 +++++++++++++++++++--------- nbmolviz/viewers/orbital_viewer.py | 1 + 11 files changed, 60 insertions(+), 20 deletions(-) rename NOTICE => NOTICES (99%) diff --git a/NOTICE b/NOTICES similarity index 99% rename from NOTICE rename to NOTICES index fb86c4b..eea1a5c 100644 --- a/NOTICE +++ b/NOTICES @@ -51,3 +51,6 @@ CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. + + + Python diff --git a/nbmolviz/install.py b/nbmolviz/install.py index fc58d94..f7003af 100644 --- a/nbmolviz/install.py +++ b/nbmolviz/install.py @@ -1,4 +1,4 @@ -from __future__ import print_function, absolute_import, division +from __future__ import print_function, absolute_import, division, unicode_literals from future.builtins import * from future import standard_library standard_library.install_aliases() @@ -170,8 +170,9 @@ def get_installed_versions(pyname, getversion): def lift_iopub_rate_limit(): - import textwrap from jupyter_core import paths as jupypaths + from .utils import indent + config_dir = jupypaths.jupyter_config_dir() nbcfgfile = os.path.join(config_dir, 'jupyter_notebook_config.py') backup_basepath = nbcfgfile+'.bak' @@ -218,7 +219,7 @@ def lift_iopub_rate_limit(): modstream.write(IOPUB_LINES) print('The following lines lines were added to the bottom of %s:' % nbcfgfile) - print(textwrap.indent(IOPUB_LINES, ' > '), end='') + print(indent(IOPUB_LINES, ' > '), end='') print("\nThese changes will take effect the next time Jupyter is launched.") @@ -229,7 +230,7 @@ def activate(flags): if exc.returncode == 2: raise PermissionError( ('ERROR - failed to enable the widget extensions with %s.' % flags) + - ' Try rerunning the command with \"sudo\"!') + ' Try rerunning the command with \"sudo\"!') else: raise diff --git a/nbmolviz/mdtconfig/compute.py b/nbmolviz/mdtconfig/compute.py index 127929f..47ab718 100644 --- a/nbmolviz/mdtconfig/compute.py +++ b/nbmolviz/mdtconfig/compute.py @@ -1,4 +1,4 @@ -from __future__ import print_function, absolute_import, division +from __future__ import print_function, absolute_import, division, unicode_literals from future.builtins import * from future import standard_library standard_library.install_aliases() diff --git a/nbmolviz/mdtconfig/docker.py b/nbmolviz/mdtconfig/docker.py index 7352ec4..59a1028 100644 --- a/nbmolviz/mdtconfig/docker.py +++ b/nbmolviz/mdtconfig/docker.py @@ -1,4 +1,4 @@ -from __future__ import print_function, absolute_import, division +from __future__ import print_function, absolute_import, division, unicode_literals from future.builtins import * from future import standard_library standard_library.install_aliases() diff --git a/nbmolviz/mdtconfig/images.py b/nbmolviz/mdtconfig/images.py index 8428c6b..1d65dfe 100644 --- a/nbmolviz/mdtconfig/images.py +++ b/nbmolviz/mdtconfig/images.py @@ -1,5 +1,5 @@ # -*- coding: utf-8 -*- -from __future__ import print_function, absolute_import, division +from __future__ import print_function, absolute_import, division, unicode_literals from future.builtins import * from future import standard_library standard_library.install_aliases() diff --git a/nbmolviz/mdtconfig/interfaces.py b/nbmolviz/mdtconfig/interfaces.py index a4f16cf..db06588 100644 --- a/nbmolviz/mdtconfig/interfaces.py +++ b/nbmolviz/mdtconfig/interfaces.py @@ -1,4 +1,5 @@ -from __future__ import print_function, absolute_import, division +# -*- coding: utf-8 -*- +from __future__ import print_function, absolute_import, division, unicode_literals from future.builtins import * from future import standard_library standard_library.install_aliases() diff --git a/nbmolviz/mdtconfig/visualization.py b/nbmolviz/mdtconfig/visualization.py index f848df7..1b123db 100644 --- a/nbmolviz/mdtconfig/visualization.py +++ b/nbmolviz/mdtconfig/visualization.py @@ -1,5 +1,5 @@ # -*- coding: utf-8 -*- -from __future__ import print_function, absolute_import, division +from __future__ import print_function, absolute_import, division, unicode_literals from future.builtins import * from future import standard_library standard_library.install_aliases() diff --git a/nbmolviz/uielements/configurator.py b/nbmolviz/uielements/configurator.py index a7bbf66..81d349f 100644 --- a/nbmolviz/uielements/configurator.py +++ b/nbmolviz/uielements/configurator.py @@ -95,8 +95,13 @@ def _pretty_print_config(self): def cleanse(v): if isinstance(v, (float,int)): return v else: return str(v) - return yaml.dump({k: cleanse(v) for k, v in self.paramlist.items()}, - default_flow_style=False) + + to_print = {} + for k, s in self.selectors.items(): + if s.paramdef.relevance is None or s.paramdef.relevance(self.paramlist): + to_print[k] = cleanse(self.paramlist[k]) + + return yaml.dump(to_print, default_flow_style=False) def show_relevant_fields(self): for s in self.selectors.values(): diff --git a/nbmolviz/utils.py b/nbmolviz/utils.py index 062b660..2d4da00 100644 --- a/nbmolviz/utils.py +++ b/nbmolviz/utils.py @@ -70,6 +70,25 @@ def translate_color(color, prefix='0x'): return color +def indent(text, prefix, predicate=None): + """Adds 'prefix' to the beginning of selected lines in 'text'. + If 'predicate' is provided, 'prefix' will only be added to the lines + where 'predicate(line)' is True. If 'predicate' is not provided, + it will default to adding 'prefix' to all non-empty lines that do not + consist solely of whitespace characters. + + BACKPORTED from python 3.7 without modification. + """ + if predicate is None: + def predicate(line): + return line.strip() + + def prefixed_lines(): + for line in text.splitlines(True): + yield (prefix + line if predicate(line) else line) + return ''.join(prefixed_lines()) + + class JSObject(object): """This is a convenient python reference to a javascript object. Really, it just stores a string""" diff --git a/nbmolviz/viewers/graph_viewer.py b/nbmolviz/viewers/graph_viewer.py index 67ff7d8..d7a64df 100644 --- a/nbmolviz/viewers/graph_viewer.py +++ b/nbmolviz/viewers/graph_viewer.py @@ -23,7 +23,6 @@ import ipywidgets as ipy import itertools -import moldesign as mdt from moldesign import utils from moldesign import units as u @@ -62,8 +61,8 @@ def __init__(self, atoms, self.atoms = getattr(atoms, 'atoms', atoms) if not _forcebig and len(self.atoms) > self.MAXATOMS: - raise ValueError('Refusing to draw more than 200 atoms in 2D visualization. ' - 'Override this with _forcebig=True') + raise ValueError('Refusing to draw more than %s atoms in 2D ' % self.MAXATOMS + + ' visualization. Override this with _forcebig=True') if names is None: names = [] @@ -87,7 +86,7 @@ def __init__(self, atoms, super().__init__(layout=ipy.Layout(width=str(width), height=str(height))) - if display: dsp.display(self) + if display: dsp(self) def __reduce__(self): """These don't get passed around, @@ -136,8 +135,10 @@ def set_atom_style(self, atoms=None, fill_color=None, outline_color=None): else: indices = list(map(self.get_atom_index, atoms)) spec = {} - if fill_color is not None: spec['fill'] = translate_color(fill_color, prefix='#') - if outline_color is not None: spec['stroke'] = translate_color(outline_color, prefix='#') + if fill_color is not None: + spec['fill'] = translate_color(fill_color, prefix='#') + if outline_color is not None: + spec['stroke'] = translate_color(outline_color, prefix='#') self.viewer('setAtomStyle', [indices, spec]) def set_bond_style(self, bonds, color=None, width=None, dash_length=None, opacity=None): @@ -175,9 +176,6 @@ def highlight_atoms(self, atoms): indices = list(map(self.get_atom_index, atoms)) self.viewer('updateHighlightAtoms', [indices]) - def get_atom_index(self, atom): - raise NotImplemented("This method must be implemented by the interface class") - def set_click_callback(self, callback=None, enabled=True): """ :param callback: Callback can have signature (), (trait_name), (trait_name,old), or (trait_name,old,new) @@ -202,6 +200,7 @@ def set_colors(self, colormap): for color, atoms in colormap.items(): self.set_color(atoms=atoms, color=color) + def _charge_str(q): q = q.value_in(u.q_e) if q == 0: @@ -301,6 +300,17 @@ def draw_contacts(self, group1, group2, radius=2.25 * u.angstrom, self.set_bond_label([atom1, atom2], text='%.1f ang'%dst.value_in('angstrom'),size=8) + def draw_3d_distances(self, color='purple', max_opacity=1.0): + with self.hold_trait_notifications(): + for edge in self.graph['links']: + a1 = self.atoms[edge['source']] + a2 = self.atoms[edge['target']] + distance = a1.distance(a2) + self.set_bond_style([[a1,a2]], + width=1, opacity=max_opacity * self.dmax / distance, + color=color) + self.send_state('graph') + def make_contact_view(entity, view_radius=5.0*u.angstrom, contact_radius=2.25*u.angstrom, diff --git a/nbmolviz/viewers/orbital_viewer.py b/nbmolviz/viewers/orbital_viewer.py index 442f08a..c3ebbd8 100644 --- a/nbmolviz/viewers/orbital_viewer.py +++ b/nbmolviz/viewers/orbital_viewer.py @@ -1,3 +1,4 @@ +# -*- coding: utf-8 -*- from __future__ import print_function, absolute_import, division, unicode_literals from future.builtins import * from future import standard_library From cb155f472995f5c393333a9deefd489d4b04bed6 Mon Sep 17 00:00:00 2001 From: Aaron Virshup Date: Fri, 8 Sep 2017 13:05:45 -0700 Subject: [PATCH 09/24] Fix python 2 installation; some installation tweaks - unpinned MDT version - even though it's a requirement, installing nbmolviz should never change the MDT version. --- NOTICES | 285 ++++++++++++++++++++++++++++++++++++--- nbmolviz/widget_utils.py | 3 +- requirements.txt | 2 +- setup.py | 5 +- 4 files changed, 271 insertions(+), 24 deletions(-) diff --git a/NOTICES b/NOTICES index eea1a5c..60327a0 100644 --- a/NOTICES +++ b/NOTICES @@ -1,20 +1,4 @@ -NBMolViz incorporates code from 3DMol.js, d3.js and PyQuante2 - - 3DMol.js ---------------------- -3DMol.js is copyright (c) 2014, University of Pittsburgh and contributors -Source file: nbmolviz/static/3Dmol.js -Description: this is modified version of the 3DMol.js library. - It has been modified to add the "forceRedraw" function. -License file: nbmolviz/static/3dmol/LICENSE - - D3.js ---------------------- -D3.js is copyright (c) 2010-2016 Mike Bostock -Source file: js/node_modules/nbmolviz2d/node_modules/d3/build/d3.node.js -Description: This is the official version distributed via npm. -Project: https://github.com/d3/d3 -License file: js/node_modules/nbmolviz2d/node_modules/d3/LICENSE +NBMolViz incorporates code from PyQuante2 and the cPython standard library PyQuante2 --------------------- @@ -53,4 +37,269 @@ OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. - Python + + Python +-------------------------------- +Copyright (c) 2001, 2002, 2003, 2004, 2005, 2006, 2007, 2008, 2009, 2010, +2011, 2012, 2013, 2014, 2015, 2016 Python Software Foundation; All Rights +Reserved +SOURCE CODE: nbmolviz/utils.py (`indent` function) +DESCRIPTION: backports of Python 3 functions +WEBSITE: https://www.python.org +LICENSE: + +A. HISTORY OF THE SOFTWARE +========================== + +Python was created in the early 1990s by Guido van Rossum at Stichting +Mathematisch Centrum (CWI, see http://www.cwi.nl) in the Netherlands +as a successor of a language called ABC. Guido remains Python's +principal author, although it includes many contributions from others. + +In 1995, Guido continued his work on Python at the Corporation for +National Research Initiatives (CNRI, see http://www.cnri.reston.va.us) +in Reston, Virginia where he released several versions of the +software. + +In May 2000, Guido and the Python core development team moved to +BeOpen.com to form the BeOpen PythonLabs team. In October of the same +year, the PythonLabs team moved to Digital Creations, which became +Zope Corporation. In 2001, the Python Software Foundation (PSF, see +https://www.python.org/psf/) was formed, a non-profit organization +created specifically to own Python-related Intellectual Property. +Zope Corporation was a sponsoring member of the PSF. + +All Python releases are Open Source (see http://www.opensource.org for +the Open Source Definition). Historically, most, but not all, Python +releases have also been GPL-compatible; the table below summarizes +the various releases. + + Release Derived Year Owner GPL- + from compatible? (1) + + 0.9.0 thru 1.2 1991-1995 CWI yes + 1.3 thru 1.5.2 1.2 1995-1999 CNRI yes + 1.6 1.5.2 2000 CNRI no + 2.0 1.6 2000 BeOpen.com no + 1.6.1 1.6 2001 CNRI yes (2) + 2.1 2.0+1.6.1 2001 PSF no + 2.0.1 2.0+1.6.1 2001 PSF yes + 2.1.1 2.1+2.0.1 2001 PSF yes + 2.1.2 2.1.1 2002 PSF yes + 2.1.3 2.1.2 2002 PSF yes + 2.2 and above 2.1.1 2001-now PSF yes + +Footnotes: + +(1) GPL-compatible doesn't mean that we're distributing Python under + the GPL. All Python licenses, unlike the GPL, let you distribute + a modified version without making your changes open source. The + GPL-compatible licenses make it possible to combine Python with + other software that is released under the GPL; the others don't. + +(2) According to Richard Stallman, 1.6.1 is not GPL-compatible, + because its license has a choice of law clause. According to + CNRI, however, Stallman's lawyer has told CNRI's lawyer that 1.6.1 + is "not incompatible" with the GPL. + +Thanks to the many outside volunteers who have worked under Guido's +direction to make these releases possible. + + +B. TERMS AND CONDITIONS FOR ACCESSING OR OTHERWISE USING PYTHON +=============================================================== + +PYTHON SOFTWARE FOUNDATION LICENSE VERSION 2 +-------------------------------------------- + +1. 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All rights reserved. + +Permission to use, copy, modify, and distribute this software and its +documentation for any purpose and without fee is hereby granted, +provided that the above copyright notice appear in all copies and that +both that copyright notice and this permission notice appear in +supporting documentation, and that the name of Stichting Mathematisch +Centrum or CWI not be used in advertising or publicity pertaining to +distribution of the software without specific, written prior +permission. + +STICHTING MATHEMATISCH CENTRUM DISCLAIMS ALL WARRANTIES WITH REGARD TO +THIS SOFTWARE, INCLUDING ALL IMPLIED WARRANTIES OF MERCHANTABILITY AND +FITNESS, IN NO EVENT SHALL STICHTING MATHEMATISCH CENTRUM BE LIABLE +FOR ANY SPECIAL, INDIRECT OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES +WHATSOEVER RESULTING FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN +ACTION OF CONTRACT, NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT +OF OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE. + diff --git a/nbmolviz/widget_utils.py b/nbmolviz/widget_utils.py index 866faa5..76d449b 100644 --- a/nbmolviz/widget_utils.py +++ b/nbmolviz/widget_utils.py @@ -87,7 +87,8 @@ def print_extension_warnings(stream=sys.stdout): if not enabled: if installed: - warnings.append('- the "{dep}" notebook extension is not enabled. ') + warnings.append('- the "{dep}" notebook extension is not enabled.' + .format(dep=dep)) if dep == 'nbmolviz': expected_py_version = pkg_resources.parse_version(_NBMOLVIZ_EXPECTED_VERSION) diff --git a/requirements.txt b/requirements.txt index a7c0e14..bdb8e27 100644 --- a/requirements.txt +++ b/requirements.txt @@ -1,7 +1,7 @@ future ipywidgets >= 7.0 ipython >= 5.0 -moldesign >= 0.8rc1 +moldesign # no version specified here so that we don't overwrite user's installed version notebook >= 4.2 matplotlib >= 2.0 numpy diff --git a/setup.py b/setup.py index 19ed1f5..0cebf67 100644 --- a/setup.py +++ b/setup.py @@ -1,8 +1,6 @@ # Adapted from https://github.com/jupyter/widget-cookiecutter from __future__ import print_function - -from builtins import str import os import shutil import sys @@ -201,7 +199,6 @@ def run(self): author_email='moleculardesigntoolkit@autodesk.com', description='Notebook Molecular Visualization: ' 'ipywidgets-based molecular visualization for molecular structures', - keywords=KEYWORDS -) + keywords=KEYWORDS) setup(**args) From bc7b97e51e02a54c4c1a31cc9343c1fb712f5ef3 Mon Sep 17 00:00:00 2001 From: Aaron Virshup Date: Fri, 8 Sep 2017 13:14:22 -0700 Subject: [PATCH 10/24] Refactor image check, clean up docker UI layout --- nbmolviz/mdtconfig/docker.py | 7 ++++--- nbmolviz/mdtconfig/images.py | 15 +++------------ 2 files changed, 7 insertions(+), 15 deletions(-) diff --git a/nbmolviz/mdtconfig/docker.py b/nbmolviz/mdtconfig/docker.py index 59a1028..9d74f1e 100644 --- a/nbmolviz/mdtconfig/docker.py +++ b/nbmolviz/mdtconfig/docker.py @@ -32,9 +32,10 @@ class DockerConfig(VBox): def __init__(self): self.client = None self.warning = ipy.HTML(value=SPINNER) + self.devmode_label = ipy.Label("Use local docker images (developer mode)", + layout=ipy.Layout(width='fit-content')) self.devmode_button = ipy.Checkbox(value=mdt.compute.config.devmode, - description="Use local docker images (developer mode)", - layout=ipy.Layout(width='100%')) + layout=ipy.Layout(width='fit-content')) self.devmode_button.observe(self.set_devmode, 'value') self.engine_config_description = ipy.HTML('Docker host with protocol and port' @@ -64,7 +65,7 @@ def __init__(self): HBox([self._reset_config_button, self._apply_changes_button, self._save_changes_button]), - self.devmode_button, + HBox([self.devmode_label, self.devmode_button]), self.image_box] self.reset_config() super().__init__(children=self.children) diff --git a/nbmolviz/mdtconfig/images.py b/nbmolviz/mdtconfig/images.py index 1d65dfe..b5ad3e6 100644 --- a/nbmolviz/mdtconfig/images.py +++ b/nbmolviz/mdtconfig/images.py @@ -152,22 +152,13 @@ def _reactivate_button(self): self.button.style.font_weight = '400' self.button.style.button_color = '#9feeb2' - def _set_status_value(self): - from docker import errors - + from moldesign.compute import image_present if self._client is None: self.status.value = 'n/a' else: - try: - imginfo = self._client.inspect_image(self.image) - except errors.ImageNotFound: - if self._err: - self.status.value = WARNING - else: - self.status.value = MISSING - else: - self.status.value = INSTALLED + installed = image_present(self._client, self.image) + self.status.value = INSTALLED if installed else WARNING def _watch_pull_logs(self, stream): found = set() From 74901632e9ec4ca6efc4f9bcf4458d004a170157 Mon Sep 17 00:00:00 2001 From: Aaron Virshup Date: Fri, 8 Sep 2017 13:15:05 -0700 Subject: [PATCH 11/24] ResidueSelector now selects residues (by default) --- nbmolviz/widgets/selection.py | 1 + 1 file changed, 1 insertion(+) diff --git a/nbmolviz/widgets/selection.py b/nbmolviz/widgets/selection.py index 2fe6ae5..d80a8f3 100644 --- a/nbmolviz/widgets/selection.py +++ b/nbmolviz/widgets/selection.py @@ -160,6 +160,7 @@ class ResidueSelector(SelBase): def __init__(self, mol): super().__init__(mol) + self.viewer.selection_type = 'Residue' self.selection_type = ipy.Dropdown(description='Clicks select:', value=self.viewer.selection_type, From c277a9e8592df48bb2f1946d157860ba992f06c0 Mon Sep 17 00:00:00 2001 From: Aaron Virshup Date: Fri, 8 Sep 2017 18:20:57 -0700 Subject: [PATCH 12/24] Handle markdown changelog --- nbmolviz/mdtconfig/compute.py | 39 +++++++++++++---------------------- requirements.txt | 1 + 2 files changed, 15 insertions(+), 25 deletions(-) diff --git a/nbmolviz/mdtconfig/compute.py b/nbmolviz/mdtconfig/compute.py index 47ab718..9714ca3 100644 --- a/nbmolviz/mdtconfig/compute.py +++ b/nbmolviz/mdtconfig/compute.py @@ -85,32 +85,21 @@ def _makelink(url, text): text=text) -class ChangeLog(HBox): +class ChangeLog(VBox): def __init__(self): - from pip._vendor.packaging import version + import markdown super().__init__() self.version = ipy.HTML('
') - self.textarea = ipy.Textarea(layout=ipy.Layout(width='700px', height='300px')) + self.textarea = ipy.HTML(layout=ipy.Layout(width='700px', height='300px')) threading.Thread(target=self.version_check).start() - p1 = os.path.join(mdt.PACKAGEPATH, "HISTORY.rst") - p2 = os.path.join(mdt.PACKAGEPATH, "..", "HISTORY.rst") - if os.path.exists(p1): - path = p1 - elif os.path.exists(p2): - path = p2 - else: - path = None - - if path is not None: - with open(path, 'r') as infile: - self.textarea.value = infile.read() - else: - self.textarea.value = 'HISTORY.rst not found' - - self.textarea.disabled = True + path = os.path.join(mdt.PACKAGEPATH, "HISTORY.md") + with open(path, 'r') as infile: + html = markdown.markdown(infile.read()) + self.textarea.value = '%s' % html + self.children = (self.version, self.textarea) def version_check(self): @@ -126,9 +115,11 @@ def version_check(self): latest = version.parse(pypi.package_releases('moldesign')[0]) current = version.parse(mdt.__version__) if current >= latest: - self.version.value = 'Up to date. Latest release: %s' % latest + self.version.value = (INSTALLED + + u'You\'re using an up-to-date release of MDT.' + u' Latest release: %s
' % latest) else: - self.version.value = ''.join(('New release available! ', + self.version.value = ''.join(('There\'s a newer version of MDT available! ', '
Installed: ' '%s' % current, @@ -136,10 +127,8 @@ def version_check(self): '%s ' % latest, '
Install it by running ' - '' - 'pip install -U moldesign or ' - '' - 'conda install -U moldesign')) + 'pip install moldesign==%s or ' % latest, + 'conda install -U moldesign
')) except Exception as e: self.version.value = 'Failed update check: %s' % e diff --git a/requirements.txt b/requirements.txt index bdb8e27..89288c8 100644 --- a/requirements.txt +++ b/requirements.txt @@ -1,6 +1,7 @@ future ipywidgets >= 7.0 ipython >= 5.0 +markdown moldesign # no version specified here so that we don't overwrite user's installed version notebook >= 4.2 matplotlib >= 2.0 From cbb5fb238172264d38d8b9fd49edb3b4ce317f79 Mon Sep 17 00:00:00 2001 From: Aaron Virshup Date: Tue, 19 Sep 2017 15:50:32 -0700 Subject: [PATCH 13/24] Add codeship build --- codeship-services.yml | 5 +++++ codeship-steps.yml | 6 ++++++ deployment/Dockerfile.build | 10 ++++++++++ 3 files changed, 21 insertions(+) create mode 100644 deployment/Dockerfile.build diff --git a/codeship-services.yml b/codeship-services.yml index e69de29..b719ce1 100644 --- a/codeship-services.yml +++ b/codeship-services.yml @@ -0,0 +1,5 @@ +builder: + build: + dockerfile: ./deployment/Dockerfile.build + context: ./ + diff --git a/codeship-steps.yml b/codeship-steps.yml index e69de29..d813562 100644 --- a/codeship-steps.yml +++ b/codeship-steps.yml @@ -0,0 +1,6 @@ +- name: build + service: builder + type: serial + steps: + - name: build_sdist + command: python setup.py sdist \ No newline at end of file diff --git a/deployment/Dockerfile.build b/deployment/Dockerfile.build new file mode 100644 index 0000000..12090dc --- /dev/null +++ b/deployment/Dockerfile.build @@ -0,0 +1,10 @@ +FROM continuumio/miniconda3:4.3.14 + +# Install requirements +RUN conda install git nodejs + +# Finally, install the actual package +ADD . /opt/notebook-molecular-visualization +WORKDIR /opt/notebook-molecular-visualization +RUN cd js && npm install +RUN python setup.py jsdeps \ No newline at end of file From dba5267d2480419683fd630eaa8539a6632e52f3 Mon Sep 17 00:00:00 2001 From: Aaron Virshup Date: Mon, 25 Sep 2017 16:44:47 -0700 Subject: [PATCH 14/24] Upgrade to m3d4react 0.4.5 and pin d3 to 4.10.0 --- js/package-lock.json | 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"https://registry.npmjs.org/yargs/-/yargs-3.10.0.tgz", + "integrity": "sha1-9+572FfdfB0tOMDnTvvWgdFDH9E=", + "dev": true, + "requires": { + "camelcase": "1.2.1", + "cliui": "2.1.0", + "decamelize": "1.2.0", + "window-size": "0.1.0" + } + } + } + } + } +} diff --git a/js/package.json b/js/package.json index d166e42..f85e8b1 100644 --- a/js/package.json +++ b/js/package.json @@ -23,9 +23,10 @@ "webpack": "^1.12.14" }, "dependencies": { + "d3": "4.10.0", "jupyter-js-widgets": "^2.1.4", "molecule-2d-for-react": "^0.2.3", - "molecule-3d-for-react": "^0.4.2", + "molecule-3d-for-react": "^0.4.5", "react": "^15.3.2", "react-dom": "^15.3.2", "underscore": "^1.8.3" From 529b2163e12b4a8c704b8e15e707b5d7b6936945 Mon Sep 17 00:00:00 2001 From: Aaron Virshup Date: Wed, 11 Oct 2017 16:51:13 -0700 Subject: [PATCH 15/24] More build cleanup --- Dockerfile | 6 ++++-- deployment/Dockerfile.build | 2 -- deployment/run_notebook.sh | 2 +- nbmolviz/install.py | 10 ++++++++-- nbmolviz/mdtconfig/docker.py | 7 +++---- 5 files changed, 16 insertions(+), 11 deletions(-) diff --git a/Dockerfile b/Dockerfile index bd4dd2d..762f64d 100644 --- a/Dockerfile +++ b/Dockerfile @@ -3,10 +3,10 @@ FROM continuumio/miniconda3:4.3.14 # Install requirements RUN conda install -c openbabel openbabel RUN conda install -c omnia biopython parmed -RUN conda install jupyter -RUN pip install "moldesign==0.8.0b3" +RUN conda install jupyter git ADD requirements.txt /opt/requirements.txt +RUN pip install --pre moldesign # probably need to invalidate cache at this level RUN pip install -r /opt/requirements.txt # This disables notebook security until we can figure out a way to pass runtime tokens @@ -26,3 +26,5 @@ RUN jupyter nbextension install --sys-prefix --py widgetsnbextension \ && jupyter nbextension enable --sys-prefix --py nbmolviz EXPOSE 8888 + +ENTRYPOINT deployment/run_notebook.sh diff --git a/deployment/Dockerfile.build b/deployment/Dockerfile.build index 12090dc..bf33a0a 100644 --- a/deployment/Dockerfile.build +++ b/deployment/Dockerfile.build @@ -6,5 +6,3 @@ RUN conda install git nodejs # Finally, install the actual package ADD . /opt/notebook-molecular-visualization WORKDIR /opt/notebook-molecular-visualization -RUN cd js && npm install -RUN python setup.py jsdeps \ No newline at end of file diff --git a/deployment/run_notebook.sh b/deployment/run_notebook.sh index 4b17a19..ea5b1f1 100755 --- a/deployment/run_notebook.sh +++ b/deployment/run_notebook.sh @@ -1,3 +1,3 @@ #!/bin/bash -jupyter notebook --ip=127.0.0.1 --no-browser --port=8888 --allow-root $@ +jupyter notebook --ip=0.0.0.0 --no-browser --port=8888 --allow-root $@ diff --git a/nbmolviz/install.py b/nbmolviz/install.py index f7003af..c48014c 100644 --- a/nbmolviz/install.py +++ b/nbmolviz/install.py @@ -65,8 +65,8 @@ def location_writable(): confpath = config_paths[pathname] extpath = ext_paths[pathname] - confpath = confpath if os.path.exists(confpath) else os.path.dirname(confpath) - extpath = extpath if os.path.exists(extpath) else os.path.dirname(extpath) + confpath = _get_first_parent_directory(confpath) + extpath = _get_first_parent_directory(extpath) writable[pathname] = ( os.access(confpath, os.W_OK | os.X_OK) and @@ -74,6 +74,12 @@ def location_writable(): return writable +def _get_first_parent_directory(path): + while not os.path.exists(path): + path = os.path.dirname(path) + return path + + def preferred_install_location(): versions = get_installed_versions('nbmolviz', True) for loc in 'environment user system'.split(): diff --git a/nbmolviz/mdtconfig/docker.py b/nbmolviz/mdtconfig/docker.py index 9d74f1e..e9b558c 100644 --- a/nbmolviz/mdtconfig/docker.py +++ b/nbmolviz/mdtconfig/docker.py @@ -42,9 +42,8 @@ def __init__(self): ' (e.g., http://localhost:2375).' ' If blank, this' ' defaults to the docker engine configured at ' - 'your command line.', - layout=ipy.Layout(width='100%')) - self.engine_config_value = ipy.Text('blank', layout=ipy.Layout(width='100%')) + 'your command line.') + self.engine_config_value = ipy.Text('blank', layout=ipy.Layout(width='80%')) self.engine_config_value.add_class('nbv-monospace') self.image_box = ipy.Box() @@ -65,7 +64,7 @@ def __init__(self): HBox([self._reset_config_button, self._apply_changes_button, self._save_changes_button]), - HBox([self.devmode_label, self.devmode_button]), + HBox([self.devmode_button, self.devmode_label]), self.image_box] self.reset_config() super().__init__(children=self.children) From e493cf7239198eb932690201937163288ba457c4 Mon Sep 17 00:00:00 2001 From: Aaron Virshup Date: Wed, 11 Oct 2017 20:19:20 -0700 Subject: [PATCH 16/24] Get npm to run even in Docker as root --- setup.py | 17 ++++++----------- 1 file changed, 6 insertions(+), 11 deletions(-) diff --git a/setup.py b/setup.py index 0cebf67..4ea6171 100644 --- a/setup.py +++ b/setup.py @@ -7,7 +7,7 @@ import versioneer from setuptools import setup, find_packages, Command from setuptools.command.egg_info import egg_info -from subprocess import check_call +from subprocess import check_call, CalledProcessError from distutils import log @@ -111,8 +111,7 @@ class NPM(Command): os.path.join(here, 'nbmolviz', 'static', 'extension.js'), os.path.join(here, 'nbmolviz', 'static', 'index.js'), os.path.join(here, 'nbmolviz', 'static', 'nbmolviz.css'), - verfile_path - ] + verfile_path] def initialize_options(self): pass @@ -124,14 +123,9 @@ def has_npm(self): try: check_call(['npm', '--version']) return True - except: + except (OSError, CalledProcessError): return False - def should_run_npm_install(self): - package_json = os.path.join(node_root, 'package.json') - node_modules_exists = os.path.exists(self.node_modules) - return self.has_npm() - def run(self): has_npm = self.has_npm() if not has_npm: @@ -145,9 +139,10 @@ def run(self): with open(vjson, 'w') as vjsonfile: vjsonfile.write('{"version":"%s"}\n' % VERSION) - if self.should_run_npm_install(): + if self.has_npm(): log.info("Installing build dependencies with npm. This may take a while...") - check_call(['npm', 'install'], cwd=node_root, stdout=sys.stdout, stderr=sys.stderr) + check_call(['npm', 'install', '--unsafe-perm'], + cwd=node_root, stdout=sys.stdout, stderr=sys.stderr) os.utime(self.node_modules, None) # TODO: do this with NPM/webpack, not in python From 7cbd6d7dfe1788f7f8a215c26904498bc1668418 Mon Sep 17 00:00:00 2001 From: Aaron Virshup Date: Wed, 11 Oct 2017 21:13:54 -0700 Subject: [PATCH 17/24] Add a deployment hook --- codeship-steps.yml | 8 +++++++- deployment/Dockerfile.build | 1 + deployment/publish.sh | 0 3 files changed, 8 insertions(+), 1 deletion(-) create mode 100644 deployment/publish.sh diff --git a/codeship-steps.yml b/codeship-steps.yml index d813562..b9d701a 100644 --- a/codeship-steps.yml +++ b/codeship-steps.yml @@ -3,4 +3,10 @@ type: serial steps: - name: build_sdist - command: python setup.py sdist \ No newline at end of file + command: python setup.py sdist + +- name: publish + service: builder + # matches tags that are valid PEP440 versions + tag: '^(0|[1-9]\d*)\.(0|[1-9]\d*)\.(0|[1-9]\d*)((a|rc|b)(0|[1-9]\d*))?$' + command: deployment/publish.sh diff --git a/deployment/Dockerfile.build b/deployment/Dockerfile.build index bf33a0a..5b72338 100644 --- a/deployment/Dockerfile.build +++ b/deployment/Dockerfile.build @@ -2,6 +2,7 @@ FROM continuumio/miniconda3:4.3.14 # Install requirements RUN conda install git nodejs +RUN pip install moldesign==0.8.0rc4 # Finally, install the actual package ADD . /opt/notebook-molecular-visualization diff --git a/deployment/publish.sh b/deployment/publish.sh new file mode 100644 index 0000000..e69de29 From 6f4125908fea0a192be555d40a4d2c514384bbea Mon Sep 17 00:00:00 2001 From: Aaron Virshup Date: Wed, 11 Oct 2017 21:33:43 -0700 Subject: [PATCH 18/24] Deployment prep --- .gitignore | 3 +++ codeship-services.yml | 5 +++++ codeship-steps.yml | 2 +- deployment/publish.sh | 23 +++++++++++++++++++++++ deployment/tokens.crypt | 1 + 5 files changed, 33 insertions(+), 1 deletion(-) create mode 100644 deployment/tokens.crypt diff --git a/.gitignore b/.gitignore index da2e098..bd05c81 100644 --- a/.gitignore +++ b/.gitignore @@ -13,3 +13,6 @@ node_modules VERSION VERSION.json tests/nb/gif +codeship.aes +deployment/tokens + diff --git a/codeship-services.yml b/codeship-services.yml index b719ce1..246425f 100644 --- a/codeship-services.yml +++ b/codeship-services.yml @@ -3,3 +3,8 @@ builder: dockerfile: ./deployment/Dockerfile.build context: ./ +publisher: + encrypted_env_file: deployment/tokens.crypt + build: + dockerfile: ./deployment/Dockerfile.build + context: ./ \ No newline at end of file diff --git a/codeship-steps.yml b/codeship-steps.yml index b9d701a..d1459c5 100644 --- a/codeship-steps.yml +++ b/codeship-steps.yml @@ -6,7 +6,7 @@ command: python setup.py sdist - name: publish - service: builder + service: publisher # matches tags that are valid PEP440 versions tag: '^(0|[1-9]\d*)\.(0|[1-9]\d*)\.(0|[1-9]\d*)((a|rc|b)(0|[1-9]\d*))?$' command: deployment/publish.sh diff --git a/deployment/publish.sh b/deployment/publish.sh index e69de29..93e1325 100644 --- a/deployment/publish.sh +++ b/deployment/publish.sh @@ -0,0 +1,23 @@ +#!/bin/bash + +# Publish a new release (triggered by a git tag that conforms to a PEP440 release) +# Exit 1 if there's a mismatch between the git tag and the package's version +# +# Expects to run in base directory of the repository + +# fail immediately if any command fails: +set -e + +PKG='nbmolviz' + +pyversion=$(python -m ${PKG} version | tail -n 1) + +if [ "${pyversion}" == "${CI_BRANCH}" ]; then + echo "Deploying version ${CI_BRANCH}" +else + echo "Can't publish - ${PKG} package version '${pyversion}' differs from its Git tag '${CI_BRANCH}'" + exit 1 +fi + +echo "Uploading version ${CI_BRANCH} to PyPI:" +twine upload -u ${PYPI_USER} -p ${PYPI_PASSWORD} dist/${PKG}-${pyversion}.tar.gz diff --git a/deployment/tokens.crypt b/deployment/tokens.crypt new file mode 100644 index 0000000..07e85df --- /dev/null +++ b/deployment/tokens.crypt @@ -0,0 +1 @@ +Zqc9x7efhLyMK2hQyt83/wr4HTzv6Q0ZRwyPRuZAXtSRXHI0UmJpdvittQiWP/QmAuHO33zpO4pgjs9NoB5vseTk \ No newline at end of file From 9f562183ca16db094e35193cc54d3ad69019f3bf Mon Sep 17 00:00:00 2001 From: Aaron Virshup Date: Wed, 11 Oct 2017 21:35:22 -0700 Subject: [PATCH 19/24] Fix header image for MDT configuration --- nbmolviz/mdtconfig/compute.py | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/nbmolviz/mdtconfig/compute.py b/nbmolviz/mdtconfig/compute.py index 9714ca3..19e0f44 100644 --- a/nbmolviz/mdtconfig/compute.py +++ b/nbmolviz/mdtconfig/compute.py @@ -29,7 +29,6 @@ from ..uielements.components import HBox, VBox - def configure(): from IPython.display import display display(MDTConfig()) @@ -62,7 +61,8 @@ def __init__(self): super().__init__(children=self.children) def make_header(self): - img = io.open(os.path.join(mdt.PACKAGEPATH, '_static_data/img/banner.png'), 'r+b').read() + with io.open(os.path.join(mdt.PACKAGEPATH, '_static_data/img/banner.png'), 'rb') as imfile: + img = imfile.read() encoded = base64.b64encode(img).decode('ascii') img = ''%encoded) links = [self._makelink(*args) for args in From f90002ecc6903e31abe3c2e8fe366466add3d868 Mon Sep 17 00:00:00 2001 From: Aaron Virshup Date: Wed, 11 Oct 2017 21:52:17 -0700 Subject: [PATCH 20/24] Fix build --- deployment/Dockerfile.build | 3 +++ 1 file changed, 3 insertions(+) diff --git a/deployment/Dockerfile.build b/deployment/Dockerfile.build index 5b72338..c3764d3 100644 --- a/deployment/Dockerfile.build +++ b/deployment/Dockerfile.build @@ -1,5 +1,8 @@ FROM continuumio/miniconda3:4.3.14 +RUN apt-get update \ + && apt-get install -y build-essential + # Install requirements RUN conda install git nodejs RUN pip install moldesign==0.8.0rc4 From a688b2949a1d3ffed021e1d3f83a53275af95aed Mon Sep 17 00:00:00 2001 From: Aaron Virshup Date: Wed, 11 Oct 2017 22:01:25 -0700 Subject: [PATCH 21/24] Make publish script executable --- deployment/publish.sh | 0 1 file changed, 0 insertions(+), 0 deletions(-) mode change 100644 => 100755 deployment/publish.sh diff --git a/deployment/publish.sh b/deployment/publish.sh old mode 100644 new mode 100755 From cd905391cf7ff13a966bae43fb74e2289ed0d066 Mon Sep 17 00:00:00 2001 From: Aaron Virshup Date: Wed, 11 Oct 2017 22:16:56 -0700 Subject: [PATCH 22/24] Fix publish script --- deployment/publish.sh | 7 ++++++- 1 file changed, 6 insertions(+), 1 deletion(-) diff --git a/deployment/publish.sh b/deployment/publish.sh index 93e1325..3101342 100755 --- a/deployment/publish.sh +++ b/deployment/publish.sh @@ -10,7 +10,12 @@ set -e PKG='nbmolviz' -pyversion=$(python -m ${PKG} version | tail -n 1) +pyversion=$(python -c "import ${PKG}; print(${PKG}.__version__)" | tail -n 1) + +if [[ -z ${CI_BRANCH} ]]; then + echo "Variable \"\$CI_BRANCH\" not set - cannot publish" + exit 2 +fi if [ "${pyversion}" == "${CI_BRANCH}" ]; then echo "Deploying version ${CI_BRANCH}" From 2f48c4f8682136194adcc351480cfde7b197fa37 Mon Sep 17 00:00:00 2001 From: Aaron Virshup Date: Wed, 11 Oct 2017 22:23:27 -0700 Subject: [PATCH 23/24] Install twine --- deployment/Dockerfile.build | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/deployment/Dockerfile.build b/deployment/Dockerfile.build index c3764d3..c57b6c2 100644 --- a/deployment/Dockerfile.build +++ b/deployment/Dockerfile.build @@ -5,7 +5,7 @@ RUN apt-get update \ # Install requirements RUN conda install git nodejs -RUN pip install moldesign==0.8.0rc4 +RUN pip install moldesign==0.8.0rc4 twine # Finally, install the actual package ADD . /opt/notebook-molecular-visualization From b1f22aa8507cfd17ee82d4ce8714d4e3a14703be Mon Sep 17 00:00:00 2001 From: Aaron Virshup Date: Thu, 12 Oct 2017 14:29:45 -0700 Subject: [PATCH 24/24] Mount the build artifacts appropriately --- codeship-services.yml | 6 +++++- codeship-steps.yml | 5 +---- deployment/publish.sh | 14 +++++++++++--- 3 files changed, 17 insertions(+), 8 deletions(-) diff --git a/codeship-services.yml b/codeship-services.yml index 246425f..fced88d 100644 --- a/codeship-services.yml +++ b/codeship-services.yml @@ -2,9 +2,13 @@ builder: build: dockerfile: ./deployment/Dockerfile.build context: ./ + volumes: + - ./nbmv-dist:/opt/nbmv-dist publisher: encrypted_env_file: deployment/tokens.crypt build: dockerfile: ./deployment/Dockerfile.build - context: ./ \ No newline at end of file + context: ./ + volumes: + - ./nbmv-dist:/opt/nbmv-dist diff --git a/codeship-steps.yml b/codeship-steps.yml index d1459c5..22e6e68 100644 --- a/codeship-steps.yml +++ b/codeship-steps.yml @@ -1,9 +1,6 @@ - name: build service: builder - type: serial - steps: - - name: build_sdist - command: python setup.py sdist + command: bash -c "python setup.py sdist && cp -r dist /opt/nbmv-dist" - name: publish service: publisher diff --git a/deployment/publish.sh b/deployment/publish.sh index 3101342..e077768 100755 --- a/deployment/publish.sh +++ b/deployment/publish.sh @@ -10,13 +10,21 @@ set -e PKG='nbmolviz' -pyversion=$(python -c "import ${PKG}; print(${PKG}.__version__)" | tail -n 1) - if [[ -z ${CI_BRANCH} ]]; then echo "Variable \"\$CI_BRANCH\" not set - cannot publish" exit 2 fi +ARTIFACT=/opt/nbmv-dist/dist/${PKG}-${CI_BRANCH}.tar.gz + +if [ ! -f $ARTIFACT ]; then + echo "No build artifact found! Expected ${ARTIFACT}" + exit 3 +fi + +pip install ${ARTIFACT} +pyversion=$(python -c "import ${PKG}; print(${PKG}.__version__)" | tail -n 1) + if [ "${pyversion}" == "${CI_BRANCH}" ]; then echo "Deploying version ${CI_BRANCH}" else @@ -25,4 +33,4 @@ else fi echo "Uploading version ${CI_BRANCH} to PyPI:" -twine upload -u ${PYPI_USER} -p ${PYPI_PASSWORD} dist/${PKG}-${pyversion}.tar.gz +twine upload -u ${PYPI_USER} -p ${PYPI_PASSWORD} ${ARTIFACT}