Update github main

.gitlab-ci.yml

@@ -35,15 +35,15 @@ authors:
 # Test containers scripts are up to date
 containers:
   stage: initial
-  image: containers.ligo.org/lscsoft/bilby/v2-bilby-python310
+  image: containers.ligo.org/lscsoft/bilby/v2-bilby-python311
   script:
     - cd containers
     - python write_dockerfiles.py #HACK
     # Fail if differences exist. If this fails, you may need to run
     # write_dockerfiles.py and commit the changes.
     - git diff --exit-code
     - cp env-template.yml env.yml
-    - echo "  - python=3.10" >> env.yml
+    - echo "  - python=3.11" >> env.yml
     - mamba env create -f env.yml -n test --dry-run
 
 .test-python: &test-python
@@ -70,10 +70,6 @@ containers:
           ${script} --help;
       done
 
-basic-3.9:
-  <<: *test-python
-  image: python:3.9
-
 basic-3.10:
   <<: *test-python
   image: python:3.10
@@ -82,17 +78,17 @@ basic-3.11:
   <<: *test-python
   image: python:3.11
 
+basic-3.12:
+  <<: *test-python
+  image: python:3.12
+
 .test-samplers-import: &test-samplers-import
   stage: initial
   script:
     - python -m pip install .
     - *list-env
     - pytest test/test_samplers_import.py -v
 
-import-samplers-3.9:
-  <<: *test-samplers-import
-  image: containers.ligo.org/lscsoft/bilby/v2-bilby-python39
-
 import-samplers-3.10:
   <<: *test-samplers-import
   image: containers.ligo.org/lscsoft/bilby/v2-bilby-python310
@@ -101,6 +97,10 @@ import-samplers-3.11:
   <<: *test-samplers-import
   image: containers.ligo.org/lscsoft/bilby/v2-bilby-python311
 
+import-samplers-3.12:
+  <<: *test-samplers-import
+  image: containers.ligo.org/lscsoft/bilby/v2-bilby-python312
+
 .precommits: &precommits
   stage: initial
   script:
@@ -112,19 +112,19 @@ import-samplers-3.11:
     # Run precommits (flake8, spellcheck, isort, no merge conflicts, etc)
     - pre-commit run --all-files --verbose --show-diff-on-failure
 
-precommits-py3.10:
+precommits-py3.11:
   <<: *precommits
-  image: containers.ligo.org/lscsoft/bilby/v2-bilby-python310
+  image: containers.ligo.org/lscsoft/bilby/v2-bilby-python311
   variables:
-    CACHE_DIR: ".pip310"
-    PYVERSION: "python310"
+    CACHE_DIR: ".pip311"
+    PYVERSION: "python311"
 
 install:
   stage: initial
   parallel:
     matrix:
       - EXTRA: [gw, mcmc, all]
-  image: containers.ligo.org/lscsoft/bilby/v2-bilby-python310
+  image: containers.ligo.org/lscsoft/bilby/v2-bilby-python311
   script:
     - pip install .[$EXTRA]
 
@@ -138,15 +138,15 @@ install:
 
     - pytest --cov=bilby --durations 10
 
-python-3.9:
-  <<: *unit-test
-  needs: ["basic-3.9"]
-  image: containers.ligo.org/lscsoft/bilby/v2-bilby-python39
-
 python-3.10:
   <<: *unit-test
-  needs: ["basic-3.10", "precommits-py3.10"]
+  needs: ["basic-3.10"]
   image: containers.ligo.org/lscsoft/bilby/v2-bilby-python310
+
+python-3.11:
+  <<: *unit-test
+  needs: ["basic-3.11", "precommits-py3.11"]
+  image: containers.ligo.org/lscsoft/bilby/v2-bilby-python311
   after_script:
     - coverage html
     - coverage xml
@@ -160,10 +160,10 @@ python-3.10:
       - htmlcov/
     expire_in: 30 days
 
-python-3.11:
+python-3.12:
   <<: *unit-test
-  needs: ["basic-3.11"]
-  image: containers.ligo.org/lscsoft/bilby/v2-bilby-python311
+  needs: ["basic-3.12"]
+  image: containers.ligo.org/lscsoft/bilby/v2-bilby-python312
 
 .test-sampler: &test-sampler
   stage: test
@@ -172,25 +172,25 @@ python-3.11:
     - *list-env
     - pytest test/integration/sampler_run_test.py --durations 10 -v
 
-python-3.9-samplers:
-  <<: *test-sampler
-  needs: ["basic-3.9"]
-  image: containers.ligo.org/lscsoft/bilby/v2-bilby-python39
-
 python-3.10-samplers:
   <<: *test-sampler
-  needs: ["basic-3.10", "precommits-py3.10"]
+  needs: ["basic-3.10"]
   image: containers.ligo.org/lscsoft/bilby/v2-bilby-python310
 
 python-3.11-samplers:
   <<: *test-sampler
-  needs: ["basic-3.11"]
+  needs: ["basic-3.11", "precommits-py3.11"]
   image: containers.ligo.org/lscsoft/bilby/v2-bilby-python311
 
-integration-tests-python-3.10:
+python-3.12-samplers:
+  <<: *test-sampler
+  needs: ["basic-3.12"]
+  image: containers.ligo.org/lscsoft/bilby/v2-bilby-python312
+
+integration-tests-python-3.11:
   stage: test
-  image: containers.ligo.org/lscsoft/bilby/v2-bilby-python310
-  needs: ["basic-3.10", "precommits-py3.10"]
+  image: containers.ligo.org/lscsoft/bilby/v2-bilby-python311
+  needs: ["basic-3.11", "precommits-py3.11"]
   only:
     - schedules
   script:
@@ -208,26 +208,26 @@ integration-tests-python-3.10:
     - *list-env
     - pytest test/gw/plot_test.py
 
-plotting-python-3.9:
-  <<: *plotting
-  image: containers.ligo.org/lscsoft/bilby/v2-bilby-python39
-  needs: ["basic-3.9"]
-
 plotting-python-3.10:
   <<: *plotting
   image: containers.ligo.org/lscsoft/bilby/v2-bilby-python310
-  needs: ["basic-3.10", "precommits-py3.10"]
+  needs: ["basic-3.10"]
 
 plotting-python-3.11:
   <<: *plotting
   image: containers.ligo.org/lscsoft/bilby/v2-bilby-python311
-  needs: ["basic-3.11"]
+  needs: ["basic-3.11", "precommits-py3.11"]
+
+plotting-python-3.12:
+  <<: *plotting
+  image: containers.ligo.org/lscsoft/bilby/v2-bilby-python312
+  needs: ["basic-3.12"]
 
 # ------------------- Docs stage -------------------------------------------
 
 docs:
   stage: docs
-  image: containers.ligo.org/lscsoft/bilby/v2-bilby-python310
+  image: containers.ligo.org/lscsoft/bilby/v2-bilby-python311
   before_script:
     - python -m ipykernel install
   script:
@@ -248,7 +248,7 @@ docs:
 
 pages:
   stage: deploy
-  needs: ["docs", "python-3.10"]
+  needs: ["docs", "python-3.11"]
   script:
     - mkdir public/
     - mv htmlcov/ public/
@@ -280,11 +280,6 @@ pages:
     - docker image tag v3-bilby-$PYVERSION containers.ligo.org/lscsoft/bilby/v2-bilby-$PYVERSION:latest
     - docker image push containers.ligo.org/lscsoft/bilby/v2-bilby-$PYVERSION:latest
 
-build-python39-container:
-  <<: *build-container
-  variables:
-    PYVERSION: "python39"
-
 build-python310-container:
   <<: *build-container
   variables:
@@ -295,6 +290,11 @@ build-python311-container:
   variables:
     PYVERSION: "python311"
 
+build-python312-container:
+  <<: *build-container
+  variables:
+    PYVERSION: "python312"
+
 pypi-release:
   stage: deploy
   image: containers.ligo.org/lscsoft/bilby/v2-bilby-python310

AUTHORS.md

@@ -16,6 +16,7 @@ Bruce Edelman
 Carl-Johan Haster
 Cecilio Garcia-Quiros
 Charlie Hoy
+Chentao Yang
 Christopher Philip Luke Berry
 Christos Karathanasis
 Colm Talbot

bilby/bilby_mcmc/sampler.py

@@ -388,7 +388,9 @@ def read_current_state(self):
             If true, resume file was successfully loaded, otherwise false
 
         """
-        if os.path.isfile(self.resume_file) is False:
+        if os.path.isfile(self.resume_file) is False or not os.path.getsize(
+            self.resume_file
+        ):
             return False
         import dill
 

bilby/core/sampler/base_sampler.py

@@ -463,7 +463,7 @@ def _time_likelihood(self, n_evaluations=100):
             logger.info("Unable to measure single likelihood time")
         else:
             logger.info(
-                f"Single likelihood evaluation took {self._log_likelihood_eval_time:.3e} s"
+                f"Single likelihood evaluation took {log_likelihood_eval_time:.3e} s"
             )
         return log_likelihood_eval_time
 

bilby/core/sampler/dynesty.py

@@ -3,6 +3,7 @@
 import os
 import sys
 import time
+import warnings
 
 import numpy as np
 from pandas import DataFrame
@@ -677,12 +678,21 @@ def _run_external_sampler_with_checkpointing(self):
         chain of nested samples within dynesty and have to be removed before
         restarting the sampler.
         """
+
         logger.debug("Running sampler with checkpointing")
 
         old_ncall = self.sampler.ncall
         sampler_kwargs = self.sampler_function_kwargs.copy()
+        warnings.filterwarnings(
+            "ignore",
+            message="The sampling was stopped short due to maxiter/maxcall limit*",
+            category=UserWarning,
+            module="dynesty.sampler",
+        )
         while True:
             self.finalize_sampler_kwargs(sampler_kwargs)
+            if getattr(self.sampler, "added_live", False):
+                self.sampler._remove_live_points()
             self.sampler.run_nested(**sampler_kwargs)
             if self.sampler.ncall == old_ncall:
                 break
@@ -697,8 +707,8 @@ def _run_external_sampler_with_checkpointing(self):
             if last_checkpoint_s > self.check_point_delta_t:
                 self.write_current_state()
                 self.plot_current_state()
-            if getattr(self.sampler, "added_live", False):
-                self.sampler._remove_live_points()
+        if getattr(self.sampler, "added_live", False):
+            self.sampler._remove_live_points()
 
         self.sampler.run_nested(**sampler_kwargs)
         self.write_current_state()
@@ -736,7 +746,10 @@ def read_saved_state(self, continuing=False):
         if os.path.isfile(self.resume_file):
             logger.info(f"Reading resume file {self.resume_file}")
             with open(self.resume_file, "rb") as file:
-                sampler = dill.load(file)
+                try:
+                    sampler = dill.load(file)
+                except EOFError:
+                    sampler = None
 
                 if not hasattr(sampler, "versions"):
                     logger.warning(

bilby/core/sampler/emcee.py

@@ -1,7 +1,6 @@
 import os
 import shutil
 from collections import namedtuple
-from shutil import copyfile
 
 import numpy as np
 from packaging import version
@@ -311,7 +310,11 @@ def sampler(self):
         """
         if hasattr(self, "_sampler"):
             pass
-        elif self.resume and os.path.isfile(self.checkpoint_info.sampler_file):
+        elif (
+            self.resume
+            and os.path.isfile(self.checkpoint_info.sampler_file)
+            and os.path.getsize(self.checkpoint_info.sampler_file)
+        ):
             import dill
 
             logger.info(
@@ -329,16 +332,19 @@ def sampler(self):
     def write_chains_to_file(self, sample):
         chain_file = self.checkpoint_info.chain_file
         temp_chain_file = chain_file + ".temp"
-        if os.path.isfile(chain_file):
-            copyfile(chain_file, temp_chain_file)
         if self.prerelease:
             points = np.hstack([sample.coords, sample.blobs])
         else:
             points = np.hstack([sample[0], np.array(sample[3])])
-        with open(temp_chain_file, "a") as ff:
-            for ii, point in enumerate(points):
-                ff.write(self.checkpoint_info.chain_template.format(ii, *point))
-        shutil.move(temp_chain_file, chain_file)
+        data_to_write = "\n".join(
+            self.checkpoint_info.chain_template.format(ii, *point)
+            for ii, point in enumerate(points)
+        )
+        with open(temp_chain_file, "w") as ff:
+            ff.write(data_to_write)
+        with open(temp_chain_file, "rb") as ftemp, open(chain_file, "ab") as fchain:
+            shutil.copyfileobj(ftemp, fchain)
+        os.remove(temp_chain_file)
 
     @property
     def _previous_iterations(self):

bilby/core/sampler/kombine.py

@@ -166,7 +166,11 @@ def sampler_chain(self):
         return self.sampler.chain[:nsteps, :, :]
 
     def check_resume(self):
-        return self.resume and os.path.isfile(self.checkpoint_info.sampler_file)
+        return (
+            self.resume
+            and os.path.isfile(self.checkpoint_info.sampler_file)
+            and os.path.getsize(self.checkpoint_info.sampler_file) > 0
+        )
 
     @signal_wrapper
     def run_sampler(self):

bilby/core/sampler/ptemcee.py

@@ -415,7 +415,11 @@ def setup_sampler(self):
             # This is a very ugly hack to support numpy>=1.24
             ptemcee.sampler.np.float = float
 
-        if os.path.isfile(self.resume_file) and self.resume is True:
+        if (
+            os.path.isfile(self.resume_file)
+            and os.path.getsize(self.resume_file)
+            and self.resume is True
+        ):
             import dill
 
             logger.info(f"Resume data {self.resume_file} found")
@@ -513,7 +517,7 @@ def run_sampler(self):
         logger.info("Starting to sample")
 
         while True:
-            for (pos0, log_posterior, log_likelihood) in sampler.sample(
+            for pos0, log_posterior, log_likelihood in sampler.sample(
                 self.pos0,
                 storechain=False,
                 iterations=self.convergence_inputs.niterations_per_check,