Attempt to fix HDF5ExtError (#157)

* change HistoryHdf5 file to read to avoid concurrent writing in HDFStore

doc/bibliography/tyssue.bib

@@ -3451,5 +3451,39 @@ @article{Bidensityindependentrigiditytransition2015
   author = {Bi, Dapeng and Lopez, J. H. and Schwarz, J. M. and Manning, M. Lisa}
 }
 
+@article{Lardennoisactinbasedviscoplasticlock2019,
+  langid = {english},
+  title = {An Actin-Based Viscoplastic Lock Ensures Progressive Body-Axis Elongation},
+  issn = {1476-4687},
+  url = {https://www.nature.com/articles/s41586-019-1509-4},
+  doi = {10.1038/s41586-019-1509-4},
+  abstract = {Molecular analysis and mathematical modelling are combined to identify a network of factors that account for viscoplastic deformation in elongation of Caenorhabditis elegans during embryonic development.},
+  journaltitle = {Nature},
+  shortjournal = {Nature},
+  urldate = {2019-08-30},
+  date = {2019-08-28},
+  pages = {1-5},
+  author = {Lardennois, Alicia and P\'asti, Gabriella and Ferraro, Teresa and Llense, Flora and Mahou, Pierre and Pontabry, Julien and Rodriguez, David and Kim, Samantha and Ono, Shoichiro and Beaurepaire, Emmanuel and Gally, Christelle and Labouesse, Michel},
+  file = {/home/guillaume/.mozilla/firefox/14u1jeb7.default-1392277802592/zotero/storage/LM8X8TZP/s41586-019-1509-4.html}
+}
+
+@article{ChenExtracellularmatrixstiffness2019,
+  langid = {english},
+  title = {Extracellular Matrix Stiffness Cues Junctional Remodeling for {{3D}} Tissue Elongation},
+  volume = {10},
+  issn = {2041-1723},
+  url = {https://www.nature.com/articles/s41467-019-10874-x},
+  doi = {10.1038/s41467-019-10874-x},
+  abstract = {The extracellular matrix can shape developing organs, but how external forces direct intercellular morphogenesis is unclear. Here, the authors use 3D imaging to show that elongation of the Drosophila egg chamber involves polarized cell reorientation signalled by changes in stiffness of the surrounding extracellular matrix.},
+  number = {1},
+  journaltitle = {Nature Communications},
+  shortjournal = {Nat Commun},
+  urldate = {2019-08-30},
+  date = {2019-07-26},
+  pages = {1-15},
+  author = {Chen, Dong-Yuan and Crest, Justin and Streichan, Sebastian J. and Bilder, David},
+  file = {/home/guillaume/.mozilla/firefox/14u1jeb7.default-1392277802592/zotero/storage/7PIYA6CG/Chen et al. - 2019 - Extracellular matrix stiffness cues junctional rem.pdf;/home/guillaume/.mozilla/firefox/14u1jeb7.default-1392277802592/zotero/storage/LPS26KHN/s41467-019-10874-x.html}
+}
+
 @preamble{ "\ifdefined\DeclarePrefChars\DeclarePrefChars{'’-}\else\fi " }
 

tyssue/core/history.py

@@ -48,7 +48,7 @@ def __init__(self, sheet, save_every=None, dt=None, extra_cols=None):
 
         self.sheet = sheet
 
-        self.time = 0.
+        self.time = 0.0
         self.index = 0
         if save_every is not None:
             self.save_every = save_every
@@ -151,16 +151,13 @@ def record(self, to_record=None, time_stamp=None):
                 cols = self.columns[element]
                 df = self.sheet.datasets[element][cols].reset_index(drop=False)
                 if not "time" in cols:
-                    times = pd.Series(
-                        np.ones((df.shape[0],)) * self.time, name="time")
-                    df = pd.concat(
-                        [df, times], ignore_index=False, axis=1, sort=False)
+                    times = pd.Series(np.ones((df.shape[0],)) * self.time, name="time")
+                    df = pd.concat([df, times], ignore_index=False, axis=1, sort=False)
                 if self.time in hist["time"]:
                     # erase previously recorded time point
                     hist = hist[hist["time"] != self.time]
 
-                hist = pd.concat(
-                    [hist, df], ignore_index=True, axis=0, sort=False)
+                hist = pd.concat([hist, df], ignore_index=True, axis=0, sort=False)
 
                 self.datasets[element] = hist
 
@@ -260,14 +257,15 @@ def __init__(
                         break
         if sheet is None:
             last = self.time_stamps[-1]
-            with pd.HDFStore(self.hf5file, "a") as file:
+            with pd.HDFStore(self.hf5file, "r") as file:
                 keys = file.keys()
             if "\cell" in keys:
                 sheet = Epithelium
 
         History.__init__(self, sheet, save_every, dt, extra_cols)
-        self.dtypes = {k: df[self.columns[k]].dtypes
-                       for k, df in sheet.datasets.items()}
+        self.dtypes = {
+            k: df[self.columns[k]].dtypes for k, df in sheet.datasets.items()
+        }
 
     @classmethod
     def from_archive(cls, hf5file, columns=None, eptm_class=None):
@@ -316,34 +314,36 @@ def record(self, to_record=None, time_stamp=None):
         if time_stamp is not None:
             self.time = time_stamp
         else:
-            self.time += 1.
+            self.time += 1.0
 
         dtypes_ = {k: df.dtypes for k, df in self.sheet.datasets.items()}
 
         for element, df in self.sheet.datasets.items():
             diff_col = set(dtypes_[element].keys()).difference(
-                set(self.dtypes[element].keys()))
+                set(self.dtypes[element].keys())
+            )
             if diff_col:
                 warnings.warn(
-                    "New columns {} will not be saved in the {} table".format(diff_col, element))
+                    "New columns {} will not be saved in the {} table".format(
+                        diff_col, element
+                    )
+                )
             else:
                 if dtypes_[element].to_dict() != self.dtypes[element].to_dict():
                     raise ValueError(
-                        "There is a change of datatype in {} table".format(element))
+                        "There is a change of datatype in {} table".format(element)
+                    )
 
         if (self.save_every is None) or (
             self.index % (int(self.save_every / self.dt)) == 0
         ):
             for element, df in self.sheet.datasets.items():
-                times = pd.Series(
-                    np.ones((df.shape[0],)) * self.time, name="time")
+                times = pd.Series(np.ones((df.shape[0],)) * self.time, name="time")
                 df = df[self.columns[element]]
-                df = pd.concat([df, times], ignore_index=False,
-                               axis=1, sort=False)
+                df = pd.concat([df, times], ignore_index=False, axis=1, sort=False)
 
                 with pd.HDFStore(self.hf5file, "a") as file:
-                    file.append(key=element, value=df,
-                                data_columns=["time"])
+                    file.append(key=element, value=df, data_columns=["time"])
 
         self.index += 1