Rename hash_() -> hashfunc() and raise warning when using hash_()

Author: tritemio

notebooks/PyBroMo - 1. Simulate 3D trajectories - single core.ipynb

@@ -77,7 +77,7 @@
    "source": [
     "# Initialize the random state\n",
     "rs = np.random.RandomState(seed=1)\n",
-    "print('Initial random state:', pbm.hash_(rs.get_state()))\n",
+    "print('Initial random state:', pbm.hashfunc(rs.get_state()))\n",
     "\n",
     "# Simulation time step (seconds)\n",
     "t_step = 0.5e-6\n",
@@ -107,7 +107,7 @@
     "S = pbm.ParticlesSimulation(t_step=t_step, t_max=t_max, \n",
     "                            particles=P, box=box, psf=psf)\n",
     "\n",
-    "print('Current random state:', pbm.hash_(rs.get_state()))"
+    "print('Current random state:', pbm.hashfunc(rs.get_state()))"
    ]
   },
   {
@@ -214,7 +214,7 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "print('Current random state:', pbm.hash_(rs.get_state()))"
+    "print('Current random state:', pbm.hashfunc(rs.get_state()))"
    ]
   },
   {
@@ -233,7 +233,7 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "print('Current random state:', pbm.hash_(rs.get_state()))"
+    "print('Current random state:', pbm.hashfunc(rs.get_state()))"
    ]
   },
   {
@@ -367,7 +367,7 @@
     "        plt.plot(t, em_ip, label='P%d' % ip)\n",
     "    ax.set_xlabel('Time (ms)')\n",
     "    \n",
-    "    rs_hash = pbm.hash_(S.traj_group._v_attrs['init_random_state'])[:3]\n",
+    "    rs_hash = pbm.hashfunc(S.traj_group._v_attrs['init_random_state'])[:3]\n",
     "    ax.set_title('%ds ID-EID: %d-%d, sim rs = %s, part rs = %s' %\\\n",
     "              (s, S.ID, S.EID, rs_hash, S.particles.rs_hash[:3]))\n",
     "    ax.legend(bbox_to_anchor=(1.03, 1), loc=2, borderaxespad=0.)\n",

notebooks/PyBroMo - A1. Reference - Data format and internals.ipynb

@@ -580,7 +580,7 @@
     "    print ('\\t%s' % attr)\n",
     "    attr_data = repr(node._v_attrs[attr])\n",
     "    if len(attr_data) > 300:\n",
-    "        attr_data = hash_(node._v_attrs[attr])\n",
+    "        attr_data = hashfunc(node._v_attrs[attr])\n",
     "    print (\"\\t    %s\" % attr_data)"
    ]
   },
@@ -876,7 +876,7 @@
     "        print ('\\t%s' % attr)\n",
     "        attr_data = repr(node._v_attrs[attr])\n",
     "        if len(attr_data) > 300:\n",
-    "            attr_data = pbm.hash_(node._v_attrs[attr])\n",
+    "            attr_data = pbm.hashfunc(node._v_attrs[attr])\n",
     "        print (\"\\t    %s\" % attr_data)\n",
     "        \n",
     "print ('\\n>> Attributes in %s:\\n' % group)\n",

notebooks/PyBroMo - B.1 Disk-single-core - Generate photon timestamps.ipynb

@@ -109,7 +109,7 @@
    "source": [
     "# Get the random state at the end of the diffusion simulation\n",
     "saved_rs_state = S.traj_group._v_attrs['last_random_state']\n",
-    "pbm.hash_(saved_rs_state)"
+    "pbm.hashfunc(saved_rs_state)"
    ]
   },
   {

pybromo/__init__.py

@@ -16,6 +16,17 @@
 
 from .utils import hdf5
 
-from .diffusion import Box, Particles, ParticlesSimulation, hash_
+from .diffusion import Box, Particles, ParticlesSimulation, hashfunc
 from .psflib import GaussianPSF, NumericPSF
 from .timestamps import TimestampSimulation
+
+import warnings
+
+
+def deprecation(message):
+    warnings.warn(message, FutureWarning, stacklevel=2)
+
+
+def hash_(x):
+    deprecation('The function `hash_` is deprecated, please use `hashfunc` instead.')
+    return hashfunc(x)

pybromo/timestamps.py

@@ -13,7 +13,7 @@
 from pathlib import Path
 import phconvert as phc
 
-from .diffusion import hash_
+from .diffusion import hashfunc
 from ._version import get_versions
 __version__ = get_versions()['version']
 
@@ -268,7 +268,7 @@ def filepath(self):
     def _calc_hash_da(self, rs):
         """Compute hash of D and A timestamps for single-step D+A case.
         """
-        self.hash_d = hash_(rs.get_state())[:6]
+        self.hash_d = hashfunc(rs.get_state())[:6]
         self.hash_a = self.hash_d
 
     def run(self, rs, overwrite=True, skip_existing=False, path=None,
@@ -291,7 +291,7 @@ def run(self, rs, overwrite=True, skip_existing=False, path=None,
         header = ' - Mixture Simulation:'
 
         # Donor timestamps hash is from the input RandomState
-        self.hash_d = hash_(rs.get_state())[:6]   # needed by merge_da()
+        self.hash_d = hashfunc(rs.get_state())[:6]   # needed by merge_da()
         print('%s Donor timestamps -    %s' % (header, ctime()), flush=True)
         self.S.simulate_timestamps_mix(
             populations=self.populations,
@@ -304,7 +304,7 @@ def run(self, rs, overwrite=True, skip_existing=False, path=None,
         # donor + acceptor timestamps given the input random state.
         ts_d, _, _ = self.S.get_timestamp_data(self.name_timestamps_d)
         rs.set_state(ts_d.attrs['last_random_state'])
-        self.hash_a = hash_(rs.get_state())[:6]   # needed by merge_da()
+        self.hash_a = hashfunc(rs.get_state())[:6]   # needed by merge_da()
         print('\n%s Acceptor timestamps - %s' % (header, ctime()), flush=True)
         self.S.simulate_timestamps_mix(
             populations=self.populations,