Branch to update to new dgl version

.github/workflows/CI.yaml

@@ -29,10 +29,11 @@ jobs:
  strategy:
  fail-fast: false
  matrix:
- os: ['macos', 'ubuntu']
+ os: ['ubuntu','macos']
  python-version:
- - "3.9"
+ - "3.11"
  - "3.10"
+ - "3.9"
 
  env:
  OPENMM: ${{ matrix.cfg.openmm }}

devtools/conda-envs/espaloma.yaml

@@ -1,7 +1,6 @@
 name: espaloma-test
 channels:
  - conda-forge
- - dglteam
  - openeye
 dependencies:
  # Base dependencies
@@ -20,9 +19,7 @@ dependencies:
  - openmmforcefields >=0.11.2
  - tqdm
  - pydantic <2 # We need our deps to fix this
- # Pytorch
- - pytorch>=1.8.0
- - dgl <1
+ - dgl =1.1.0
  # Testing
  - pytest
  - pytest-cov

espaloma/app/experiment.py

@@ -201,7 +201,7 @@ def test(self):
  # from time to time
  # make it just one giant graph
  # g = list(self.data)
- # g = dgl.batch_hetero(g)
+ # g = dgl.batch(g)
  # g = g.to(self.device)
 
  if self.states is None:

espaloma/data/dataset.py

@@ -293,13 +293,13 @@ def batch(graphs):
  import dgl
 
  if all(isinstance(graph, esp.graphs.graph.Graph) for graph in graphs):
- return dgl.batch_hetero([graph.heterograph for graph in graphs])
+ return dgl.batch([graph.heterograph for graph in graphs])
 
  elif all(isinstance(graph, dgl.DGLGraph) for graph in graphs):
  return dgl.batch(graphs)
 
  elif all(isinstance(graph, dgl.DGLHeteroGraph) for graph in graphs):
- return dgl.batch_hetero(graphs)
+ return dgl.batch(graphs)
 
  else:
  raise RuntimeError(

espaloma/mm/energy.py

@@ -361,7 +361,7 @@ def energy_in_graph(
  {
  "%s_in_g"
  % term: (
- dgl.function.copy_src(src="u%s" % suffix, out="m_%s" % term),
+ dgl.function.copy_u(u="u%s" % suffix, out="m_%s" % term),
  dgl.function.sum(
  msg="m_%s" % term, out="u_%s%s" % (term, suffix)
  ),
@@ -462,31 +462,31 @@ def forward(self, g):
  g.multi_update_all(
  {
  "n2_as_0_in_n3": (
- dgl.function.copy_src("u", "m_u_0"),
+ dgl.function.copy_u("u", "m_u_0"),
  dgl.function.sum("m_u_0", "u_left"),
  ),
  "n2_as_1_in_n3": (
- dgl.function.copy_src("u", "m_u_1"),
+ dgl.function.copy_u("u", "m_u_1"),
  dgl.function.sum("m_u_1", "u_right"),
  ),
  "n2_as_0_in_n4": (
- dgl.function.copy_src("u", "m_u_0"),
+ dgl.function.copy_u("u", "m_u_0"),
  dgl.function.sum("m_u_0", "u_bond_left"),
  ),
  "n2_as_1_in_n4": (
- dgl.function.copy_src("u", "m_u_1"),
+ dgl.function.copy_u("u", "m_u_1"),
  dgl.function.sum("m_u_1", "u_bond_center"),
  ),
  "n2_as_2_in_n4": (
- dgl.function.copy_src("u", "m_u_2"),
+ dgl.function.copy_u("u", "m_u_2"),
  dgl.function.sum("m_u_2", "u_bond_right"),
  ),
  "n3_as_0_in_n4": (
- dgl.function.copy_src("u", "m3_u_0"),
+ dgl.function.copy_u("u", "m3_u_0"),
  dgl.function.sum("m3_u_0", "u_angle_left"),
  ),
  "n3_as_1_in_n4": (
- dgl.function.copy_src("u", "m3_u_1"),
+ dgl.function.copy_u("u", "m3_u_1"),
  dgl.function.sum("m3_u_1", "u_angle_right"),
  ),
  },

espaloma/mm/geometry.py

@@ -188,7 +188,7 @@ def geometry_in_graph(g):
  **{
  "n1_as_%s_in_n%s"
  % (pos_idx, big_idx): (
- dgl.function.copy_src(src="xyz", out="m_xyz%s" % pos_idx),
+ dgl.function.copy_u(u="xyz", out="m_xyz%s" % pos_idx),
  dgl.function.sum(
  msg="m_xyz%s" % pos_idx, out="xyz%s" % pos_idx
  ),
@@ -199,7 +199,7 @@ def geometry_in_graph(g):
  **{
  "n1_as_%s_in_%s"
  % (pos_idx, term): (
- dgl.function.copy_src(src="xyz", out="m_xyz%s" % pos_idx),
+ dgl.function.copy_u(u="xyz", out="m_xyz%s" % pos_idx),
  dgl.function.sum(
  msg="m_xyz%s" % pos_idx, out="xyz%s" % pos_idx
  ),
@@ -210,7 +210,7 @@ def geometry_in_graph(g):
  **{
  "n1_as_%s_in_%s"
  % (pos_idx, term): (
- dgl.function.copy_src(src="xyz", out="m_xyz%s" % pos_idx),
+ dgl.function.copy_u(u="xyz", out="m_xyz%s" % pos_idx),
  dgl.function.sum(
  msg="m_xyz%s" % pos_idx, out="xyz%s" % pos_idx
  ),

espaloma/mm/nonbonded.py

@@ -48,8 +48,8 @@ def lorentz_berthelot(g, suffix=""):
  {
  "n1_as_%s_in_%s"
  % (pos_idx, term): (
- dgl.function.copy_src(
- src="epsilon%s" % suffix, out="m_epsilon"
+ dgl.function.copy_u(
+ u="epsilon%s" % suffix, out="m_epsilon"
  ),
  geometric_mean(msg="m_epsilon", out="epsilon%s" % suffix),
  )
@@ -63,7 +63,7 @@ def lorentz_berthelot(g, suffix=""):
  {
  "n1_as_%s_in_%s"
  % (pos_idx, term): (
- dgl.function.copy_src(src="sigma%s" % suffix, out="m_sigma"),
+ dgl.function.copy_u(u="sigma%s" % suffix, out="m_sigma"),
  arithmetic_mean(msg="m_sigma", out="sigma%s" % suffix),
  )
  for pos_idx in [0, 1]
@@ -94,7 +94,7 @@ def multiply_charges(g, suffix=""):
  {
  "n1_as_%s_in_%s"
  % (pos_idx, term): (
- dgl.function.copy_src(src="q%s" % suffix, out="m_q"),
+ dgl.function.copy_u(u="q%s" % suffix, out="m_q"),
  dgl.function.sum(msg="m_q", out="_q")
  # lambda node: {"q%s" % suffix: node.mailbox["m_q"].prod(dim=1)}
  )

espaloma/mm/tests/test_energy_ii.py

@@ -78,31 +78,31 @@ def forward(self, g):
  g.multi_update_all(
  {
  "n2_as_0_in_n3": (
- dgl.function.copy_src("u", "m_u_0"),
+ dgl.function.copy_u("u", "m_u_0"),
  dgl.function.sum("m_u_0", "u_left"),
  ),
  "n2_as_1_in_n3": (
- dgl.function.copy_src("u", "m_u_1"),
+ dgl.function.copy_u("u", "m_u_1"),
  dgl.function.sum("m_u_1", "u_right"),
  ),
  "n2_as_0_in_n4": (
- dgl.function.copy_src("u", "m_u_0"),
+ dgl.function.copy_u("u", "m_u_0"),
  dgl.function.sum("m_u_0", "u_bond_left"),
  ),
  "n2_as_1_in_n4": (
- dgl.function.copy_src("u", "m_u_1"),
+ dgl.function.copy_u("u", "m_u_1"),
  dgl.function.sum("m_u_1", "u_bond_center"),
  ),
  "n2_as_2_in_n4": (
- dgl.function.copy_src("u", "m_u_2"),
+ dgl.function.copy_u("u", "m_u_2"),
  dgl.function.sum("m_u_2", "u_bond_right"),
  ),
  "n3_as_0_in_n4": (
- dgl.function.copy_src("u", "m3_u_0"),
+ dgl.function.copy_u("u", "m3_u_0"),
  dgl.function.sum("m3_u_0", "u_angle_left"),
  ),
  "n3_as_1_in_n4": (
- dgl.function.copy_src("u", "m3_u_1"),
+ dgl.function.copy_u("u", "m3_u_1"),
  dgl.function.sum("m3_u_1", "u_angle_right"),
  ),
  },

espaloma/nn/readout/charge_equilibrium.py

@@ -80,7 +80,7 @@ def forward(self, g, total_charge=0.0):
  if "q_ref" in g.nodes["n1"].data:
  # get total charge
  g.update_all(
- dgl.function.copy_src(src="q_ref", out="m_q"),
+ dgl.function.copy_u(u="q_ref", out="m_q"),
  dgl.function.sum(msg="m_q", out="sum_q"),
  etype="n1_in_g",
  )
@@ -95,32 +95,32 @@ def forward(self, g, total_charge=0.0):
  )
 
  g.update_all(
- dgl.function.copy_src(src="sum_q", out="m_sum_q"),
+ dgl.function.copy_u(u="sum_q", out="m_sum_q"),
  dgl.function.sum(msg="m_sum_q", out="sum_q"),
  etype="g_has_n1",
  )
 
  # get the sum of $s^{-1}$ and $m_s^{-1}$
  g.update_all(
- dgl.function.copy_src(src="s_inv", out="m_s_inv"),
+ dgl.function.copy_u(u="s_inv", out="m_s_inv"),
  dgl.function.sum(msg="m_s_inv", out="sum_s_inv"),
  etype="n1_in_g",
  )
 
  g.update_all(
- dgl.function.copy_src(src="e_s_inv", out="m_e_s_inv"),
+ dgl.function.copy_u(u="e_s_inv", out="m_e_s_inv"),
  dgl.function.sum(msg="m_e_s_inv", out="sum_e_s_inv"),
  etype="n1_in_g",
  )
 
  g.update_all(
- dgl.function.copy_src(src="sum_s_inv", out="m_sum_s_inv"),
+ dgl.function.copy_u(u="sum_s_inv", out="m_sum_s_inv"),
  dgl.function.sum(msg="m_sum_s_inv", out="sum_s_inv"),
  etype="g_has_n1",
  )
 
  g.update_all(
- dgl.function.copy_src(src="sum_e_s_inv", out="m_sum_e_s_inv"),
+ dgl.function.copy_u(u="sum_e_s_inv", out="m_sum_e_s_inv"),
  dgl.function.sum(msg="m_sum_e_s_inv", out="sum_e_s_inv"),
  etype="g_has_n1",
  )

espaloma/nn/readout/graph_level_readout.py

@@ -53,7 +53,7 @@ def forward(self, g):
  )
 
  g.update_all(
- dgl.function.copy_src("h_global", "m"),
+ dgl.function.copy_u("h_global", "m"),
  self.pool("m", "h_global"),
  etype="n1_in_g",
  )

espaloma/nn/readout/janossy.py

@@ -104,7 +104,7 @@ def forward(self, g):
  {
  "n1_as_%s_in_n%s"
  % (relationship_idx, big_idx): (
- dgl.function.copy_src("h", "m%s" % relationship_idx),
+ dgl.function.copy_u("h", "m%s" % relationship_idx),
  dgl.function.mean(
  "m%s" % relationship_idx, "h%s" % relationship_idx
  ),
@@ -240,7 +240,7 @@ def forward(self, g):
  {
  "n1_as_%s_in_%s"
  % (relationship_idx, big_idx): (
- dgl.function.copy_src("h", "m%s" % relationship_idx),
+ dgl.function.copy_u("h", "m%s" % relationship_idx),
  dgl.function.mean(
  "m%s" % relationship_idx, "h%s" % relationship_idx
  ),
@@ -358,7 +358,7 @@ def forward(self, g):
  {
  "n1_as_%s_in_%s"
  % (relationship_idx, big_idx): (
- dgl.function.copy_src("h", "m%s" % relationship_idx),
+ dgl.function.copy_u("h", "m%s" % relationship_idx),
  dgl.function.mean(
  "m%s" % relationship_idx, "h%s" % relationship_idx
  ),
@@ -475,7 +475,7 @@ def forward(self, g):
  {
  "n1_as_%s_in_%s"
  % (relationship_idx, big_idx): (
- dgl.function.copy_src("h", "m%s" % relationship_idx),
+ dgl.function.copy_u("h", "m%s" % relationship_idx),
  dgl.function.mean(
  "m%s" % relationship_idx, "h%s" % relationship_idx
  ),