def test_save(self):
resp = self.nb_api.read('a.ipynb', 'foo')
nbcontent = json.loads(resp.text)['content']
nb = to_notebook_json(nbcontent)
ws = new_worksheet()
nb.worksheets = [ws]
ws.cells.append(new_heading_cell(u'Created by test ³'))
nbmodel= {'name': 'a.ipynb', 'path':'foo', 'content': nb}
resp = self.nb_api.save('a.ipynb', path='foo', body=json.dumps(nbmodel))
nbfile = pjoin(self.notebook_dir.name, 'foo', 'a.ipynb')
with io.open(nbfile, 'r', encoding='utf-8') as f:
newnb = read(f, format='ipynb')
self.assertEqual(newnb.worksheets[0].cells[0].source,
u'Created by test ³')
nbcontent = self.nb_api.read('a.ipynb', 'foo').json()['content']
newnb = to_notebook_json(nbcontent)
self.assertEqual(newnb.worksheets[0].cells[0].source,
u'Created by test ³')
# Save and rename
nbmodel= {'name': 'a2.ipynb', 'path':'foo/bar', 'content': nb}
resp = self.nb_api.save('a.ipynb', path='foo', body=json.dumps(nbmodel))
saved = resp.json()
self.assertEqual(saved['name'], 'a2.ipynb')
self.assertEqual(saved['path'], 'foo/bar')
assert os.path.isfile(pjoin(self.notebook_dir.name,'foo','bar','a2.ipynb'))
assert not os.path.isfile(pjoin(self.notebook_dir.name, 'foo', 'a.ipynb'))
with assert_http_error(404):
self.nb_api.read('a.ipynb', 'foo')
def test_save(self):
resp = self.nb_api.read('a.ipynb', 'foo')
nbcontent = json.loads(resp.text)['content']
nb = to_notebook_json(nbcontent)
ws = new_worksheet()
nb.worksheets = [ws]
ws.cells.append(new_heading_cell(u'Created by test ³'))
nbmodel = {'name': 'a.ipynb', 'path': 'foo', 'content': nb}
resp = self.nb_api.save(
'a.ipynb', path='foo', body=json.dumps(nbmodel))
nbfile = pjoin(self.notebook_dir.name, 'foo', 'a.ipynb')
with io.open(nbfile, 'r', encoding='utf-8') as f:
newnb = read(f, format='ipynb')
self.assertEqual(newnb.worksheets[0].cells[0].source,
u'Created by test ³')
nbcontent = self.nb_api.read('a.ipynb', 'foo').json()['content']
newnb = to_notebook_json(nbcontent)
self.assertEqual(newnb.worksheets[0].cells[0].source,
u'Created by test ³')
# Save and rename
nbmodel = {'name': 'a2.ipynb', 'path': 'foo/bar', 'content': nb}
resp = self.nb_api.save(
'a.ipynb', path='foo', body=json.dumps(nbmodel))
saved = resp.json()
self.assertEqual(saved['name'], 'a2.ipynb')
self.assertEqual(saved['path'], 'foo/bar')
assert os.path.isfile(
pjoin(self.notebook_dir.name, 'foo', 'bar', 'a2.ipynb'))
assert not os.path.isfile(
pjoin(self.notebook_dir.name, 'foo', 'a.ipynb'))
with assert_http_error(404):
self.nb_api.read('a.ipynb', 'foo')
def process_header(self, header):
""" Process a header from pandoc json """
level, attrs, contents = header
contents = self.process_inline(contents)
self._add_cell(nbf.new_heading_cell(contents,
metadata=META_SLIDE,
level=level))
def test_checkpoints(self):
resp = self.api.read('a.ipynb', 'foo')
r = self.api.new_checkpoint('a.ipynb', 'foo')
self.assertEqual(r.status_code, 201)
cp1 = r.json()
self.assertEqual(set(cp1), {'id', 'last_modified'})
self.assertEqual(r.headers['Location'].split('/')[-1], cp1['id'])
# Modify it
nbcontent = json.loads(resp.text)['content']
nb = to_notebook_json(nbcontent)
ws = new_worksheet()
nb.worksheets = [ws]
hcell = new_heading_cell('Created by test')
ws.cells.append(hcell)
# Save
nbmodel = {
'name': 'a.ipynb',
'path': 'foo',
'content': nb,
'type': 'notebook'
}
resp = self.api.save('a.ipynb', path='foo', body=json.dumps(nbmodel))
# List checkpoints
cps = self.api.get_checkpoints('a.ipynb', 'foo').json()
self.assertEqual(cps, [cp1])
nbcontent = self.api.read('a.ipynb', 'foo').json()['content']
nb = to_notebook_json(nbcontent)
self.assertEqual(nb.worksheets[0].cells[0].source, 'Created by test')
# Restore cp1
r = self.api.restore_checkpoint('a.ipynb', 'foo', cp1['id'])
self.assertEqual(r.status_code, 204)
nbcontent = self.api.read('a.ipynb', 'foo').json()['content']
nb = to_notebook_json(nbcontent)
self.assertEqual(nb.worksheets, [])
# Delete cp1
r = self.api.delete_checkpoint('a.ipynb', 'foo', cp1['id'])
self.assertEqual(r.status_code, 204)
cps = self.api.get_checkpoints('a.ipynb', 'foo').json()
self.assertEqual(cps, [])
def test_contents_manager(self):
"make sure ContentsManager returns right files (ipynb, bin, txt)."
nbdir = self.notebook_dir.name
base = self.base_url()
nb = new_notebook(name='testnb')
ws = new_worksheet()
nb.worksheets = [ws]
ws.cells.append(new_heading_cell(u'Created by test ³'))
cc1 = new_code_cell(input=u'print(2*6)')
cc1.outputs.append(new_output(output_text=u'12', output_type='stream'))
ws.cells.append(cc1)
with io.open(pjoin(nbdir, 'testnb.ipynb'), 'w',
encoding='utf-8') as f:
write(nb, f, format='ipynb')
with io.open(pjoin(nbdir, 'test.bin'), 'wb') as f:
f.write(b'\xff' + os.urandom(5))
f.close()
with io.open(pjoin(nbdir, 'test.txt'), 'w') as f:
f.write(u'foobar')
f.close()
r = requests.get(url_path_join(base, 'files', 'testnb.ipynb'))
self.assertEqual(r.status_code, 200)
self.assertIn('print(2*6)', r.text)
json.loads(r.text)
r = requests.get(url_path_join(base, 'files', 'test.bin'))
self.assertEqual(r.status_code, 200)
self.assertEqual(r.headers['content-type'], 'application/octet-stream')
self.assertEqual(r.content[:1], b'\xff')
self.assertEqual(len(r.content), 6)
r = requests.get(url_path_join(base, 'files', 'test.txt'))
self.assertEqual(r.status_code, 200)
self.assertEqual(r.headers['content-type'], 'text/plain')
self.assertEqual(r.text, 'foobar')
def test_contents_manager(self):
"make sure ContentsManager returns right files (ipynb, bin, txt)."
nbdir = self.notebook_dir.name
base = self.base_url()
nb = new_notebook(name='testnb')
ws = new_worksheet()
nb.worksheets = [ws]
ws.cells.append(new_heading_cell(u'Created by test ³'))
cc1 = new_code_cell(input=u'print(2*6)')
cc1.outputs.append(new_output(output_text=u'12', output_type='stream'))
ws.cells.append(cc1)
with io.open(pjoin(nbdir, 'testnb.ipynb'), 'w', encoding='utf-8') as f:
write(nb, f, format='ipynb')
with io.open(pjoin(nbdir, 'test.bin'), 'wb') as f:
f.write(b'\xff' + os.urandom(5))
f.close()
with io.open(pjoin(nbdir, 'test.txt'), 'w') as f:
f.write(u'foobar')
f.close()
r = requests.get(url_path_join(base, 'files', 'testnb.ipynb'))
self.assertEqual(r.status_code, 200)
self.assertIn('print(2*6)', r.text)
json.loads(r.text)
r = requests.get(url_path_join(base, 'files', 'test.bin'))
self.assertEqual(r.status_code, 200)
self.assertEqual(r.headers['content-type'], 'application/octet-stream')
self.assertEqual(r.content[:1], b'\xff')
self.assertEqual(len(r.content), 6)
r = requests.get(url_path_join(base, 'files', 'test.txt'))
self.assertEqual(r.status_code, 200)
self.assertEqual(r.headers['content-type'], 'text/plain')
self.assertEqual(r.text, 'foobar')
def setUp(self):
nbdir = self.notebook_dir.name
if not os.path.isdir(pjoin(nbdir, 'foo')):
os.mkdir(pjoin(nbdir, 'foo'))
nb = new_notebook(name='testnb')
ws = new_worksheet()
nb.worksheets = [ws]
ws.cells.append(new_heading_cell(u'Created by test ³'))
cc1 = new_code_cell(input=u'print(2*6)')
cc1.outputs.append(new_output(output_text=u'12'))
cc1.outputs.append(new_output(output_png=png_green_pixel, output_type='pyout'))
ws.cells.append(cc1)
with io.open(pjoin(nbdir, 'foo', 'testnb.ipynb'), 'w',
encoding='utf-8') as f:
write(nb, f, format='ipynb')
self.nbconvert_api = NbconvertAPI(self.base_url())
def test_checkpoints(self):
resp = self.nb_api.read('a.ipynb', 'foo')
r = self.nb_api.new_checkpoint('a.ipynb', 'foo')
self.assertEqual(r.status_code, 201)
cp1 = r.json()
self.assertEqual(set(cp1), {'id', 'last_modified'})
self.assertEqual(r.headers['Location'].split('/')[-1], cp1['id'])
# Modify it
nbcontent = json.loads(resp.text)['content']
nb = to_notebook_json(nbcontent)
ws = new_worksheet()
nb.worksheets = [ws]
hcell = new_heading_cell('Created by test')
ws.cells.append(hcell)
# Save
nbmodel = {'name': 'a.ipynb', 'path': 'foo', 'content': nb}
resp = self.nb_api.save(
'a.ipynb', path='foo', body=json.dumps(nbmodel))
# List checkpoints
cps = self.nb_api.get_checkpoints('a.ipynb', 'foo').json()
self.assertEqual(cps, [cp1])
nbcontent = self.nb_api.read('a.ipynb', 'foo').json()['content']
nb = to_notebook_json(nbcontent)
self.assertEqual(nb.worksheets[0].cells[0].source, 'Created by test')
# Restore cp1
r = self.nb_api.restore_checkpoint('a.ipynb', 'foo', cp1['id'])
self.assertEqual(r.status_code, 204)
nbcontent = self.nb_api.read('a.ipynb', 'foo').json()['content']
nb = to_notebook_json(nbcontent)
self.assertEqual(nb.worksheets, [])
# Delete cp1
r = self.nb_api.delete_checkpoint('a.ipynb', 'foo', cp1['id'])
self.assertEqual(r.status_code, 204)
cps = self.nb_api.get_checkpoints('a.ipynb', 'foo').json()
self.assertEqual(cps, [])
def setUp(self):
nbdir = self.notebook_dir.name
if not os.path.isdir(pjoin(nbdir, 'foo')):
os.mkdir(pjoin(nbdir, 'foo'))
nb = new_notebook(name='testnb')
ws = new_worksheet()
nb.worksheets = [ws]
ws.cells.append(new_heading_cell(u'Created by test ³'))
cc1 = new_code_cell(input=u'print(2*6)')
cc1.outputs.append(new_output(output_text=u'12'))
cc1.outputs.append(
new_output(output_png=png_green_pixel, output_type='pyout'))
ws.cells.append(cc1)
with io.open(pjoin(nbdir, 'foo', 'testnb.ipynb'),
'w',
encoding='utf-8') as f:
write(nb, f, format='ipynb')
self.nbconvert_api = NbconvertAPI(self.base_url())
def visit_title(self, node):
#make sure we have a valid heading level between 1 and 6
heading_level = min(self.section_level, 5) + 1
h = nbformat.new_heading_cell(source=node.astext(),
level=heading_level)
self.add_cell(h)
def visit_title(self, node):
#make sure we have a valid heading level between 1 and 6
heading_level = min(self.section_level, 5) + 1
h = nbformat.new_heading_cell(source=node.astext(),
level=heading_level)
self.add_cell(h)
def process_header(self, header):
""" Process a header from pandoc json """
level, attrs, contents = header
contents = self.process_inline(contents)
self._add_cell(
nbf.new_heading_cell(contents, metadata=META_SLIDE, level=level))
def write_notebook(pseudopath, with_eos=False, tmpfile=None):
"""
Write an ipython notebook to pseudopath.
By default, the notebook is created in the same directory
as pseudopath but with the extension `ipynb` unless `tmpfile` is set to True.
In the later case, a temporay file is created.
Args:
pseudo: Path to the pseudopotential file.
with_eos: True if EOS plots are wanted.
Returns:
The path to the ipython notebook.
See http://nbviewer.ipython.org/gist/fperez/9716279
"""
from IPython.nbformat import current as nbf
# from IPython.nbformat import v3 as nbf
# import IPython.nbformat as nbf
nb = nbf.new_notebook()
cells = [
nbf.new_heading_cell("This is an auto-generated notebook for %s" % os.path.basename(pseudopath)),
nbf.new_code_cell(
"""\
from __future__ import print_function
%matplotlib inline
import mpld3
from mpld3 import plugins as plugs
plugs.DEFAULT_PLUGINS = [plugs.Reset(), plugs.Zoom(), plugs.BoxZoom(), plugs.MousePosition()]
mpld3.enable_notebook()
import seaborn as sns
#sns.set(style="dark", palette="Set2")
sns.set(style='ticks', palette='Set2')"""
),
nbf.new_code_cell(
"""\
# Construct the pseudo object and get the DojoReport
from pymatgen.io.abinitio.pseudos import Pseudo
pseudo = Pseudo.from_file('%s')
report = pseudo.dojo_report"""
% os.path.abspath(pseudopath)
),
nbf.new_heading_cell("ONCVPSP Input File:"),
nbf.new_code_cell(
"""\
input_file = pseudo.filepath.replace(".psp8", ".in")
%cat $input_file"""
),
nbf.new_code_cell(
"""\
# Get data from the output file
from pseudo_dojo.ppcodes.oncvpsp import OncvOutputParser, PseudoGenDataPlotter
onc_parser = OncvOutputParser(pseudo.filepath.replace(".psp8", ".out"))
# Parse the file and build the plotter
onc_parser.scan()
plotter = onc_parser.make_plotter()"""
),
nbf.new_heading_cell("AE and PS radial wavefunctions $\phi(r)$:"),
nbf.new_code_cell("fig = plotter.plot_radial_wfs(show=False)"),
nbf.new_heading_cell("Arctan of the logarithmic derivatives:"),
nbf.new_code_cell("fig = plotter.plot_atan_logders(show=False)"),
nbf.new_heading_cell("Convergence in $G$-space estimated by ONCVPSP:"),
nbf.new_code_cell("fig = plotter.plot_ene_vs_ecut(show=False)"),
nbf.new_heading_cell("Projectors:"),
nbf.new_code_cell("fig = plotter.plot_projectors(show=False)"),
nbf.new_heading_cell("Core-Valence-Model charge densities:"),
nbf.new_code_cell("fig = plotter.plot_densities(show=False)"),
nbf.new_heading_cell("Local potential and $l$-dependent potentials:"),
nbf.new_code_cell("fig = plotter.plot_potentials(show=False)"),
# nbf.new_heading_cell("1-st order derivative of $v_l$ and $v_{loc}$ computed via finite differences:"),
# nbf.new_code_cell("""fig = plotter.plot_der_potentials(order=1, show=False)"""),
# nbf.new_heading_cell("2-nd order derivative of $v_l$ and $v_{loc}$ computed via finite differences:"),
# nbf.new_code_cell("""fig = plotter.plot_der_potentials(order=2, show=False)"""),
nbf.new_heading_cell("Model core charge and form factors computed by ABINIT"),
nbf.new_code_cell(
"""\
with pseudo.open_pspsfile() as psps:
psps.plot()"""
),
nbf.new_heading_cell("Convergence of the total energy:"),
nbf.new_code_cell(
"""\
# Convergence of the total energy (computed from the deltafactor runs with Wien2K equilibrium volume)
fig = report.plot_etotal_vs_ecut(show=False)"""
),
nbf.new_heading_cell("Convergence of the deltafactor results:"),
nbf.new_code_cell(
"""fig = report.plot_deltafactor_convergence(what=("dfact_meV", "dfactprime_meV"), show=False)"""
),
nbf.new_heading_cell("Convergence of $\Delta v_0$, $\Delta b_0$, and $\Delta b_1$ (deltafactor tests)"),
nbf.new_code_cell(
"""\
# Here we plot the difference wrt Wien2k results.
fig = report.plot_deltafactor_convergence(what=("-dfact_meV", "-dfactprime_meV"), show=False)"""
),
nbf.new_heading_cell("deltafactor EOS for the different cutoff energies:"),
nbf.new_code_cell("fig = report.plot_deltafactor_eos(show=False)"),
nbf.new_heading_cell("Convergence of the GBRV lattice parameters:"),
nbf.new_code_cell("fig = report.plot_gbrv_convergence(show=False)"),
nbf.new_heading_cell("Convergence of phonon frequencies at $\Gamma$:"),
nbf.new_code_cell("fig = report.plot_phonon_convergence(show=False)"),
# nbf.new_heading_cell("Comparison with the other pseudos in this table"),
# nbf.new_code_cell("""\
# from pseudo_dojo import get_pseudos
# pseudos = get_pseudos(".")
# if len(pseudos) > 1:
# pseudos.dojo_compare()"""),
]
if with_eos:
# Add EOS plots
cells.update(
[
nbf.new_heading_cell("GBRV EOS for the FCC structure:"),
nbf.new_code_cell("""fig = report.plot_gbrv_eos(struct_type="fcc", show=False)"""),
nbf.new_heading_cell("GBRV EOS for the BCC structure:"),
nbf.new_code_cell("""fig = report.plot_gbrv_eos(struct_type="bcc", show=False)"""),
]
)
# Now that we have the cells, we can make a worksheet with them and add it to the notebook:
nb["worksheets"].append(nbf.new_worksheet(cells=cells))
# Next, we write it to a file on disk that we can then open as a new notebook.
# Note: This should be as easy as: nbf.write(nb, fname), but the current api is
# a little more verbose and needs a real file-like object.
if tmpfile is None:
root, ext = os.path.splitext(pseudopath)
nbpath = root + ".ipynb"
else:
import tempfile
_, nbpath = tempfile.mkstemp(suffix=".ipynb", text=True)
with open(nbpath, "wt") as f:
nbf.write(nb, f, "ipynb")
return nbpath
def visit_title(self, node):
h = nbformat.new_heading_cell(source=node.astext())
self.add_cell(h)