Fix tests for momi intsallation on Ubuntu for py3.8

Author: noscode

.github/workflows/publication_to_pypi.yml

@@ -10,7 +10,7 @@ on:
 jobs:
   build-n-publish:
     name: Build and publish Python distributions to PyPI and TestPyPI
-    runs-on: ubuntu-18.04
+    runs-on: ubuntu-20.04
 
     steps:
     - uses: actions/checkout@master

.github/workflows/tests.yml

@@ -14,7 +14,7 @@ jobs:
     strategy:
       fail-fast: false
       matrix:
-        os: [ubuntu-20.04, windows-2019, macos-10.15]
+        os: [ubuntu-20.04, windows-2019, macos-latest]
         python-version: [3.6, 3.8]
         include:
           - os: windows-2019
@@ -102,10 +102,16 @@ jobs:
           python3 setup.py install
           cd ..
 
+      # For some reason the last version of wheel cause an error for momi installation
+      - name: Use specific version of wheel for momi installation (Linux)
+        if: runner.os == 'Linux' &&  matrix.python-version == '3.8'
+        run: |
+          python3 -m pip install wheel==0.38.4
+
       - name: Install momi engine (Linux).
         if: runner.os == 'Linux'
         run: |
-          pip3 install momi
+          python3 -m pip install momi
 
       - name: Check installations of packages.
         run: |

gadma/cli/settings_storage.py

@@ -9,7 +9,7 @@
 from ..engines import DadiEngine
 from ..engines import all_engines, all_drawing_engines, all_available_engines
 from ..models import StructureDemographicModel, CustomDemographicModel,\
-    EpochDemographicModel
+    EpochDemographicModel, TreeDemographicModel
 from ..optimizers import get_local_optimizer, get_global_optimizer
 from ..optimizers import LinearConstrain
 from ..utils import check_dir_existence, check_file_existence, abspath,\
@@ -1269,7 +1269,7 @@ def get_model(self):
                 has_dyns=create_dyns,
                 sym_migs=sym_migs,
                 frac_split=split_f,
-                migs_mask=migs_mask,
+                migs_mask=copy.deepcopy(migs_mask),
                 gen_time=gen_time,
                 theta0=theta0,
                 mutation_rate=mut_rate,
@@ -1441,8 +1441,8 @@ def get_available_engines(self, print_warnings=False):
                         continue
                 available_engines.append(engine.id)
         else:
-            assert isinstance(self.model, CustomDemographicModel)
-            available_engines.append(self.engine.id)
+            assert isinstance(model, CustomDemographicModel)
+            available_engines.append(self.engine)
         return available_engines
 
     def is_valid(self):
@@ -1454,7 +1454,7 @@ def is_valid(self):
             if self.units_of_time_in_drawing != "generations":
                 warnings.warn(
                     "Time for generation is not set. All times will be in"
-                    "generations (output and pictures)."
+                    " generations (output and pictures)."
                 )
                 self.units_of_time_in_drawing != "generations"
         if (self.input_data is None and
@@ -1563,9 +1563,9 @@ def is_valid(self):
                 )
                 self.units_of_time_in_drawing = "years"
 
-        if self.sequence_length is None and momi_available:
-            warnings.warn("Code for momi2 will not be generated as `Sequence "
-                          "length` is missed.")
+        # if self.sequence_length is None and momi_available:
+        #     warnings.warn("Code for momi2 will not be generated as `Sequence"
+        #                   " length` is missed.")
 
         # Check for sequence length if we have several chrom lengths
         if isinstance(self.sequence_length, dict):
@@ -1598,25 +1598,26 @@ def is_valid(self):
                          "specify length for chromosomes separately via dict"
         if not moments_ld_ok:
             if self.engine != "momentsLD":
-                warnings.warn("Code for momentsLD will not be generated as: "
-                              f"{reason}")
+                pass
+                # warnings.warn("Code for momentsLD will not be generated as: "
+                #               f"{reason}")
             else:
                 raise ValueError("MomentsLD requirements are not satisfied: "
                                  f"{reason}")
 
-        for engine, is_available in zip(["demes", "momi2"],
-                                        [demes_available, momi_available]):
-            if is_available:
-                if not self.Nanc_will_be_available():
-                    warnings.warn(
-                        f"Code for {engine} engine will not be generated as "
-                        "ancestral size will be missed in the dem. model. "
-                        "The following options should be set to enable it:\n"
-                        f"`Ancestral size as parameter`: True "
-                        f"(got `self.ancestral_size_as_parameter`)\nor\n"
-                        f"`Mutation rate` (got {self.mutation_rate})\n"
-                        f"`Sequence length` (got {self.sequence_length})\nor\n"
-                        f"`Theta0` (got {self.theta0})")
+        # for engine, is_available in zip(["demes", "momi2"],
+        #                                 [demes_available, momi_available]):
+        #     if is_available:
+        #         if not self.Nanc_will_be_available():
+        #             warnings.warn(
+        #                 f"Code for {engine} engine will not be generated as "
+        #                 "ancestral size will be missed in the dem. model. "
+        #                 "The following options should be set to enable it:\n"
+        #                 f"`Ancestral size as parameter`: True "
+        #                 f"(got `self.ancestral_size_as_parameter`)\nor\n"
+        #                 f"`Mutation rate` (got {self.mutation_rate})\n"
+        #                 f"`Sequence length` (got {self.sequence_length})\nor"
+        #                 f"\n`Theta0` (got {self.theta0})")
 
         if self.ld_kwargs is not None:
             if self.engine != "momentsLD":

gadma/core/core.py

@@ -63,9 +63,6 @@ def main():
     sys.stdout = StdAndFileLogger(log_file, settings_storage.silence)
     sys.stderr = StdAndFileLogger(log_file, stderr=True)
 
-    # Check what engines will be available and print warnings
-    settings_storage.get_available_engines(print_warnings=True)
-
     try:
         # Data reading
         print("Data reading")
@@ -90,6 +87,9 @@ def main():
             print(f"{bcolors.OKGREEN}--Successful bootstrap data reading--"
                   f"{bcolors.ENDC}\n")
 
+        # Check what engines will be available and print warnings
+        settings_storage.get_available_engines(print_warnings=True)
+
         # Save parameters
         settings_storage.to_files(params_file, extra_params_file)
         if not args.test:

gadma/core/core_run.py

@@ -106,7 +106,7 @@ def __init__(self, index, shared_dict, settings):
                 self.code_dir = os.path.join(self.output_dir, 'code')
                 ensure_dir_existence(self.code_dir)
                 for engine_id in self.available_engines:
-                    engine_dir = os.path.join(self.code_dir, engine.id)
+                    engine_dir = os.path.join(self.code_dir, engine_id)
                     ensure_dir_existence(engine_dir)
         # Set counters to zero for callbacks to count number of their calls
         self.draw_iter_callback_counter = 0