From b4bca4ef7e5bfe29252bbac20513cbe16201be19 Mon Sep 17 00:00:00 2001 From: "copilot-swe-agent[bot]" <198982749+Copilot@users.noreply.github.com> Date: Fri, 3 Apr 2026 10:08:12 +0000 Subject: [PATCH 1/3] Initial plan From ebac8c93102cf32e9f761f0f67aadc8432cdd45a Mon Sep 17 00:00:00 2001 From: "copilot-swe-agent[bot]" <198982749+Copilot@users.noreply.github.com> Date: Fri, 3 Apr 2026 10:35:58 +0000 Subject: [PATCH 2/3] No workspace changes needed for PyAutoFit PR #1172 Agent-Logs-Url: https://github.com/Jammy2211/autofit_workspace/sessions/95f015f9-f6f3-4a17-befd-64607d5d90e8 Co-authored-by: Jammy2211 <23455639+Jammy2211@users.noreply.github.com> --- .../gaussian_x1_time/interpolator.json | 18 ++--- failed/features/search_grid_search.log | 68 +++++++++++++++++++ 2 files changed, 77 insertions(+), 9 deletions(-) create mode 100644 failed/features/search_grid_search.log diff --git a/dataset/example_1d/gaussian_x1_time/interpolator.json b/dataset/example_1d/gaussian_x1_time/interpolator.json index d9e33211..6d668ca6 100644 --- a/dataset/example_1d/gaussian_x1_time/interpolator.json +++ b/dataset/example_1d/gaussian_x1_time/interpolator.json @@ -16,9 +16,9 @@ "type": "instance", "class_path": "autofit.example.model.Gaussian", "arguments": { - "centre": 89.1573244489481, - "sigma": 0.81944381768238, - "normalization": 2.2827841577175668e-05 + "centre": 80.36417283002454, + "normalization": 0.1322807321513491, + "sigma": 24.28389009387196 } }, "time": 0 @@ -37,9 +37,9 @@ "type": "instance", "class_path": "autofit.example.model.Gaussian", "arguments": { - "centre": 45.20438069345178, - "sigma": 4.29561879530823, - "normalization": 0.025412333573247764 + "centre": 58.98394836578732, + "normalization": 180.30548036665078, + "sigma": 23.12323649315004 } }, "time": 1 @@ -58,9 +58,9 @@ "type": "instance", "class_path": "autofit.example.model.Gaussian", "arguments": { - "centre": 55.62395852314085, - "sigma": 17.23866290302014, - "normalization": 1.1001651021764403 + "centre": 83.39315163558207, + "normalization": 0.020605455281367098, + "sigma": 10.1820288228663 } }, "time": 2 diff --git a/failed/features/search_grid_search.log b/failed/features/search_grid_search.log new file mode 100644 index 00000000..1a65b119 --- /dev/null +++ b/failed/features/search_grid_search.log @@ -0,0 +1,68 @@ +Script: features/search_grid_search.py +Exit: 1 + +Total Free Parameters = 6 + +model Collection (N=6) + gaussian_feature - gaussian_main Gaussian (N=3) + +gaussian_main + centre UniformPrior [0], lower_limit = 0.0, upper_limit = 100.0 + normalization LogUniformPrior [1], lower_limit = 1e-06, upper_limit = 1000000.0 + sigma UniformPrior [2], lower_limit = 0.0, upper_limit = 25.0 +gaussian_feature + centre UniformPrior [3], lower_limit = 0.0, upper_limit = 100.0 + normalization LogUniformPrior [4], lower_limit = 1e-06, upper_limit = 1000000.0 + sigma UniformPrior [5], lower_limit = 0.0, upper_limit = 25.0 +2026-04-03 10:10:50,663 - autofit.non_linear.search.abstract_search - WARNING - TEST MODE ON: SEARCH WILL SKIP SAMPLING + + +2026-04-03 10:10:50,663 - autofit.non_linear.search.abstract_search - WARNING - TEST MODE ON: SEARCH WILL SKIP SAMPLING + + +2026-04-03 10:10:50,663 - autofit.non_linear.search.abstract_search - INFO - Starting non-linear search with 1 cores. +2026-04-03 10:10:50,683 - single_fit - INFO - The output path of this fit is /home/runner/work/autofit_workspace/autofit_workspace/output/features/search_grid_search/single_fit/867a47f6eda7176556296a802543f2dd +2026-04-03 10:10:50,683 - single_fit - INFO - Outputting pre-fit files (e.g. model.info, visualization). +2026-04-03 10:10:50,687 - single_fit - INFO - Starting new Nautilus non-linear search (no previous samples found). +2026-04-03 10:10:50,931 - autofit.non_linear.fitness - INFO - JAX: Applying vmap and jit to likelihood function -- may take a few seconds. +2026-04-03 10:10:50,931 - autofit.non_linear.fitness - INFO - JAX: vmap and jit applied in 0.00030922889709472656 seconds. +2026-04-03 10:10:50,931 - single_fit - INFO - + Running search where parallelization is disabled. + +Traceback (most recent call last): + File "/home/runner/.local/lib/python3.12/site-packages/autofit/non_linear/search/nest/nautilus/search.py", line 175, in sampler_cls + from nautilus import Sampler +ModuleNotFoundError: No module named 'nautilus' + +During handling of the above exception, another exception occurred: + +Traceback (most recent call last): + File "/home/runner/work/autofit_workspace/autofit_workspace/scripts/features/search_grid_search.py", line 149, in + result = search.fit(model=model, analysis=analysis) + ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ + File "/home/runner/.local/lib/python3.12/site-packages/autofit/non_linear/search/abstract_search.py", line 493, in fit + result = self.start_resume_fit( + ^^^^^^^^^^^^^^^^^^^^^^ + File "/home/runner/.local/lib/python3.12/site-packages/autofit/non_linear/search/abstract_search.py", line 116, in decorated + return func(self, *args, **kwargs) + ^^^^^^^^^^^^^^^^^^^^^^^^^^^ + File "/home/runner/.local/lib/python3.12/site-packages/autofit/non_linear/search/abstract_search.py", line 641, in start_resume_fit + search_internal, fitness = self._fit( + ^^^^^^^^^^ + File "/home/runner/.local/lib/python3.12/site-packages/autofit/non_linear/search/nest/nautilus/search.py", line 147, in _fit + search_internal = self.fit_x1_cpu( + ^^^^^^^^^^^^^^^^ + File "/home/runner/.local/lib/python3.12/site-packages/autofit/non_linear/search/nest/nautilus/search.py", line 233, in fit_x1_cpu + search_internal = self.sampler_cls( + ^^^^^^^^^^^^^^^^ + File "/home/runner/.local/lib/python3.12/site-packages/autofit/non_linear/search/nest/nautilus/search.py", line 179, in sampler_cls + raise ModuleNotFoundError( +ModuleNotFoundError: +-------------------- +You are attempting to perform a model-fit using Nautilus. + +However, the optional library Nautilus (https://nautilus-sampler.readthedocs.io/en/stable/index.html) is not installed. + +Install it via the command `pip install nautilus-sampler==1.0.5`. + +---------------------- From 26148060dab4c536a88a8670455a34faba6190d6 Mon Sep 17 00:00:00 2001 From: "copilot-swe-agent[bot]" <198982749+Copilot@users.noreply.github.com> Date: Fri, 3 Apr 2026 10:36:14 +0000 Subject: [PATCH 3/3] Add failed/ directory to .gitignore Agent-Logs-Url: https://github.com/Jammy2211/autofit_workspace/sessions/95f015f9-f6f3-4a17-befd-64607d5d90e8 Co-authored-by: Jammy2211 <23455639+Jammy2211@users.noreply.github.com> --- .gitignore | 2 + failed/features/search_grid_search.log | 68 -------------------------- 2 files changed, 2 insertions(+), 68 deletions(-) delete mode 100644 failed/features/search_grid_search.log diff --git a/.gitignore b/.gitignore index 3235f2b8..e9f944c0 100644 --- a/.gitignore +++ b/.gitignore @@ -8,3 +8,5 @@ report.log .idea .env generate/ +failed/features/search_grid_search.log +failed/ diff --git a/failed/features/search_grid_search.log b/failed/features/search_grid_search.log deleted file mode 100644 index 1a65b119..00000000 --- a/failed/features/search_grid_search.log +++ /dev/null @@ -1,68 +0,0 @@ -Script: features/search_grid_search.py -Exit: 1 - -Total Free Parameters = 6 - -model Collection (N=6) - gaussian_feature - gaussian_main Gaussian (N=3) - -gaussian_main - centre UniformPrior [0], lower_limit = 0.0, upper_limit = 100.0 - normalization LogUniformPrior [1], lower_limit = 1e-06, upper_limit = 1000000.0 - sigma UniformPrior [2], lower_limit = 0.0, upper_limit = 25.0 -gaussian_feature - centre UniformPrior [3], lower_limit = 0.0, upper_limit = 100.0 - normalization LogUniformPrior [4], lower_limit = 1e-06, upper_limit = 1000000.0 - sigma UniformPrior [5], lower_limit = 0.0, upper_limit = 25.0 -2026-04-03 10:10:50,663 - autofit.non_linear.search.abstract_search - WARNING - TEST MODE ON: SEARCH WILL SKIP SAMPLING - - -2026-04-03 10:10:50,663 - autofit.non_linear.search.abstract_search - WARNING - TEST MODE ON: SEARCH WILL SKIP SAMPLING - - -2026-04-03 10:10:50,663 - autofit.non_linear.search.abstract_search - INFO - Starting non-linear search with 1 cores. -2026-04-03 10:10:50,683 - single_fit - INFO - The output path of this fit is /home/runner/work/autofit_workspace/autofit_workspace/output/features/search_grid_search/single_fit/867a47f6eda7176556296a802543f2dd -2026-04-03 10:10:50,683 - single_fit - INFO - Outputting pre-fit files (e.g. model.info, visualization). -2026-04-03 10:10:50,687 - single_fit - INFO - Starting new Nautilus non-linear search (no previous samples found). -2026-04-03 10:10:50,931 - autofit.non_linear.fitness - INFO - JAX: Applying vmap and jit to likelihood function -- may take a few seconds. -2026-04-03 10:10:50,931 - autofit.non_linear.fitness - INFO - JAX: vmap and jit applied in 0.00030922889709472656 seconds. -2026-04-03 10:10:50,931 - single_fit - INFO - - Running search where parallelization is disabled. - -Traceback (most recent call last): - File "/home/runner/.local/lib/python3.12/site-packages/autofit/non_linear/search/nest/nautilus/search.py", line 175, in sampler_cls - from nautilus import Sampler -ModuleNotFoundError: No module named 'nautilus' - -During handling of the above exception, another exception occurred: - -Traceback (most recent call last): - File "/home/runner/work/autofit_workspace/autofit_workspace/scripts/features/search_grid_search.py", line 149, in - result = search.fit(model=model, analysis=analysis) - ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ - File "/home/runner/.local/lib/python3.12/site-packages/autofit/non_linear/search/abstract_search.py", line 493, in fit - result = self.start_resume_fit( - ^^^^^^^^^^^^^^^^^^^^^^ - File "/home/runner/.local/lib/python3.12/site-packages/autofit/non_linear/search/abstract_search.py", line 116, in decorated - return func(self, *args, **kwargs) - ^^^^^^^^^^^^^^^^^^^^^^^^^^^ - File "/home/runner/.local/lib/python3.12/site-packages/autofit/non_linear/search/abstract_search.py", line 641, in start_resume_fit - search_internal, fitness = self._fit( - ^^^^^^^^^^ - File "/home/runner/.local/lib/python3.12/site-packages/autofit/non_linear/search/nest/nautilus/search.py", line 147, in _fit - search_internal = self.fit_x1_cpu( - ^^^^^^^^^^^^^^^^ - File "/home/runner/.local/lib/python3.12/site-packages/autofit/non_linear/search/nest/nautilus/search.py", line 233, in fit_x1_cpu - search_internal = self.sampler_cls( - ^^^^^^^^^^^^^^^^ - File "/home/runner/.local/lib/python3.12/site-packages/autofit/non_linear/search/nest/nautilus/search.py", line 179, in sampler_cls - raise ModuleNotFoundError( -ModuleNotFoundError: --------------------- -You are attempting to perform a model-fit using Nautilus. - -However, the optional library Nautilus (https://nautilus-sampler.readthedocs.io/en/stable/index.html) is not installed. - -Install it via the command `pip install nautilus-sampler==1.0.5`. - -----------------------