From db00c3eb3e480caf932c5cbe2e45fdfbe7047156 Mon Sep 17 00:00:00 2001 From: naik-aakash Date: Tue, 22 Oct 2024 10:01:06 +0200 Subject: [PATCH 1/7] add contributing guidelines hyperlink --- README.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/README.md b/README.md index 783a908c..d8808168 100644 --- a/README.md +++ b/README.md @@ -51,7 +51,7 @@ curl -O https://www.mtg.msm.cam.ac.uk/files/airss-0.9.3.tgz; tar -xf airss-0.9.3 # Contributing guidelines -Please follow the [contributing guidelines](docs/dev/contributing.md)! +Please follow the [contributing guidelines](https://autoatml.github.io/autoplex/dev/contributing.html)! # Workflow overview From a806041e7ccc65eb07b2489e6090f13d2a4f36fc Mon Sep 17 00:00:00 2001 From: naik-aakash Date: Tue, 22 Oct 2024 10:01:25 +0200 Subject: [PATCH 2/7] add custom header --- docs/conf.py | 1 + 1 file changed, 1 insertion(+) diff --git a/docs/conf.py b/docs/conf.py index 9233c794..f48b055f 100644 --- a/docs/conf.py +++ b/docs/conf.py @@ -76,6 +76,7 @@ napoleon_use_param = True napoleon_use_rtype = True napoleon_use_ivar = True +napoleon_custom_sections = [('Tuneable Hyperparameters', 'params_style')] # The suffix(es) of source filenames. source_suffix = { From 5c4ab8a0d1b033e67b5cb452d6f0181afb1f34a7 Mon Sep 17 00:00:00 2001 From: naik-aakash Date: Tue, 22 Oct 2024 10:02:12 +0200 Subject: [PATCH 3/7] output>return (non recognized header) --- autoplex/data/rss/flows.py | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/autoplex/data/rss/flows.py b/autoplex/data/rss/flows.py index 3da4dba8..480a1a98 100644 --- a/autoplex/data/rss/flows.py +++ b/autoplex/data/rss/flows.py @@ -117,8 +117,8 @@ def initial_rss( fit_kwargs : dict, optional Additional arguments for the machine learning fit. Default is None. - Output - ------ + Returns + ------- - test_error: float The test error of the fitted MLIP. - pre_database_dir: str From c0e411e5dd135c67469d2774ee4ee32462a84244 Mon Sep 17 00:00:00 2001 From: naik-aakash Date: Tue, 22 Oct 2024 10:22:12 +0200 Subject: [PATCH 4/7] remove duplicated --- docs/index.md | 1 - docs/user/index.md | 7 ++----- 2 files changed, 2 insertions(+), 6 deletions(-) diff --git a/docs/index.md b/docs/index.md index 12abfa65..f42fb7d4 100644 --- a/docs/index.md +++ b/docs/index.md @@ -24,7 +24,6 @@ dev/contributing :hidden: about/changelog about/contributors -about/contributing about/license ``` diff --git a/docs/user/index.md b/docs/user/index.md index d5b2a106..7ca053d8 100644 --- a/docs/user/index.md +++ b/docs/user/index.md @@ -3,9 +3,6 @@ Getting started ```{include} ../../README.md --- start-line: 3 -end-line: 52 +end-line: 54 --- -``` -# Contributing guidelines - -Please follow the [contributing guidelines](../dev/contributing.md)! +``` \ No newline at end of file From c2fc010d28e59e00851cce35db89608945633d1c Mon Sep 17 00:00:00 2001 From: naik-aakash Date: Tue, 22 Oct 2024 10:28:08 +0200 Subject: [PATCH 5/7] try defining custom header --- docs/conf.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/docs/conf.py b/docs/conf.py index f48b055f..14b1e252 100644 --- a/docs/conf.py +++ b/docs/conf.py @@ -76,7 +76,7 @@ napoleon_use_param = True napoleon_use_rtype = True napoleon_use_ivar = True -napoleon_custom_sections = [('Tuneable Hyperparameters', 'params_style')] +napoleon_custom_sections = [('Tuneable Hyperparameters', 'Parameters')] # The suffix(es) of source filenames. source_suffix = { From 637e57fea5b01b66eef47fd32bbfc4ac28adc59b Mon Sep 17 00:00:00 2001 From: naik-aakash Date: Tue, 22 Oct 2024 10:28:27 +0200 Subject: [PATCH 6/7] remove : --- autoplex/fitting/common/utils.py | 16 ++++++++-------- 1 file changed, 8 insertions(+), 8 deletions(-) diff --git a/autoplex/fitting/common/utils.py b/autoplex/fitting/common/utils.py index a2e21fcd..db85c909 100644 --- a/autoplex/fitting/common/utils.py +++ b/autoplex/fitting/common/utils.py @@ -277,8 +277,8 @@ def jace_fitting( optional dictionary with parameters for ace fitting with keys same as mlip-defaults.json. - Tuneable hyperparameters: - ------------------------- + Tuneable hyperparameters + ------------------------ order: int order of ACE. totaldegree: int @@ -461,8 +461,8 @@ def nequip_fitting( optional dictionary with parameters for nequip fitting with keys same as mlip-defaults.json. - Tuneable hyperparameters: - ------------------------- + Tuneable hyperparameters + ------------------------ r_max: float cutoff radius in length units num_layers: int @@ -733,8 +733,8 @@ def m3gnet_fitting( optional dictionary with parameters for m3gnet fitting with keys same as mlip-defaults.json. - Tuneable hyperparameters: - ------------------------- + Tuneable hyperparameters + ------------------------ exp_name: str Name of the experiment, used for saving model checkpoints and logs. results_dir: str @@ -1106,8 +1106,8 @@ def mace_fitting( optional dictionary with parameters for mace fitting with keys same as mlip-defaults.json. - Tuneable hyperparameters: - ------------------------- + Tuneable hyperparameters + ------------------------ model: str type of model to be trained config_type_weights: str From 455dcee352b8df0b95ac52618f9e75fe79400742 Mon Sep 17 00:00:00 2001 From: naik-aakash Date: Tue, 22 Oct 2024 10:37:53 +0200 Subject: [PATCH 7/7] rename Tuneable Hyperparameter to Keyword Arguments --- autoplex/fitting/common/utils.py | 16 ++++++++-------- docs/conf.py | 1 - 2 files changed, 8 insertions(+), 9 deletions(-) diff --git a/autoplex/fitting/common/utils.py b/autoplex/fitting/common/utils.py index db85c909..52945080 100644 --- a/autoplex/fitting/common/utils.py +++ b/autoplex/fitting/common/utils.py @@ -277,8 +277,8 @@ def jace_fitting( optional dictionary with parameters for ace fitting with keys same as mlip-defaults.json. - Tuneable hyperparameters - ------------------------ + Keyword Arguments + ----------------- order: int order of ACE. totaldegree: int @@ -461,8 +461,8 @@ def nequip_fitting( optional dictionary with parameters for nequip fitting with keys same as mlip-defaults.json. - Tuneable hyperparameters - ------------------------ + Keyword Arguments + ----------------- r_max: float cutoff radius in length units num_layers: int @@ -733,8 +733,8 @@ def m3gnet_fitting( optional dictionary with parameters for m3gnet fitting with keys same as mlip-defaults.json. - Tuneable hyperparameters - ------------------------ + Keyword Arguments + ----------------- exp_name: str Name of the experiment, used for saving model checkpoints and logs. results_dir: str @@ -1106,8 +1106,8 @@ def mace_fitting( optional dictionary with parameters for mace fitting with keys same as mlip-defaults.json. - Tuneable hyperparameters - ------------------------ + Keyword Arguments + ----------------- model: str type of model to be trained config_type_weights: str diff --git a/docs/conf.py b/docs/conf.py index 14b1e252..9233c794 100644 --- a/docs/conf.py +++ b/docs/conf.py @@ -76,7 +76,6 @@ napoleon_use_param = True napoleon_use_rtype = True napoleon_use_ivar = True -napoleon_custom_sections = [('Tuneable Hyperparameters', 'Parameters')] # The suffix(es) of source filenames. source_suffix = {