From 74c647507ff83a0c5f4dbb5f2a7dabed79a7224c Mon Sep 17 00:00:00 2001 From: benwandrew Date: Wed, 30 Aug 2023 13:54:01 -0400 Subject: [PATCH 01/20] docs: add skeleton for terminology.md --- docs/terminology.md | 9 +++++++++ 1 file changed, 9 insertions(+) create mode 100644 docs/terminology.md diff --git a/docs/terminology.md b/docs/terminology.md new file mode 100644 index 000000000..dd2e75f89 --- /dev/null +++ b/docs/terminology.md @@ -0,0 +1,9 @@ +# AutoRA Terminology + +The following table includes naming conventions used throughout AutoRA. + +| Term | Description | Use | +|--------------|------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------|----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------| +| Conditions | abc xyz | Experimentalist, Theorist, | +| Observations | abc xyz | Experimentalist, Theorist, | +| Model | abc xyz | Experimentalist, Theorist, | From 4ac276f91384a092cbd59fcbf0e730164ab23479 Mon Sep 17 00:00:00 2001 From: benwandrew Date: Wed, 13 Sep 2023 10:09:56 -0400 Subject: [PATCH 02/20] docs: committing outstanding changes --- docs/terminology.md | 2 ++ 1 file changed, 2 insertions(+) diff --git a/docs/terminology.md b/docs/terminology.md index dd2e75f89..14db863b9 100644 --- a/docs/terminology.md +++ b/docs/terminology.md @@ -2,6 +2,8 @@ The following table includes naming conventions used throughout AutoRA. +## Core Package + | Term | Description | Use | |--------------|------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------|----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------| | Conditions | abc xyz | Experimentalist, Theorist, | From 65886e10a800b303cf878af1b619cdc456280e17 Mon Sep 17 00:00:00 2001 From: benwandrew Date: Wed, 27 Sep 2023 08:27:59 -0400 Subject: [PATCH 03/20] docs: add full list of terms --- docs/terminology.md | 23 +++++++++++++++++------ 1 file changed, 17 insertions(+), 6 deletions(-) diff --git a/docs/terminology.md b/docs/terminology.md index 14db863b9..ef13f5bbe 100644 --- a/docs/terminology.md +++ b/docs/terminology.md @@ -2,10 +2,21 @@ The following table includes naming conventions used throughout AutoRA. -## Core Package +## [ ] -| Term | Description | Use | -|--------------|------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------|----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------| -| Conditions | abc xyz | Experimentalist, Theorist, | -| Observations | abc xyz | Experimentalist, Theorist, | -| Model | abc xyz | Experimentalist, Theorist, | +| Term | Description | Relevant Modules | +|-------------------|-------------|-------------------------------------------------| +| State | abc xyz | Core | +| StandardState | abc xyz | Core | +| Conditions | abc xyz | Experimentalists, Experiment Runners, Theorists | +| Experiment Data | abc xyz | Experiment Runners, Theorists | +| Model | abc xyz | Theorists, Experimentalists | +| Variables | abc xyz | Experimentalists, Experiment Runners, Theorists | +| Components | abc xyz | Experimentalists, Experiment Runners, Theorists | +| Experimentalist | abc xyz | Experimentalists | +| Theorist | abc xyz | Theorists | +| Experiment Runner | abc xyz | Experiment Runners | +| Wrapper | abc xyz | Experimentalists, Experiment Runners, Theorists | +| Workflow | abc xyz | Experimentalists, Experiment Runners, Theorists | +| Cycle | abc xyz | Experimentalists, Experiment Runners, Theorists | +| Cylc | abc xyz | Experimentalists, Experiment Runners, Theorists | From c3499e6ca62504431c09f2e1a8ff0318e46f11d3 Mon Sep 17 00:00:00 2001 From: benwandrew Date: Wed, 18 Oct 2023 07:12:40 -0400 Subject: [PATCH 04/20] docs: partial descriptions --- docs/terminology.md | 33 +++++++++++++++++---------------- 1 file changed, 17 insertions(+), 16 deletions(-) diff --git a/docs/terminology.md b/docs/terminology.md index ef13f5bbe..36cd65684 100644 --- a/docs/terminology.md +++ b/docs/terminology.md @@ -4,19 +4,20 @@ The following table includes naming conventions used throughout AutoRA. ## [ ] -| Term | Description | Relevant Modules | -|-------------------|-------------|-------------------------------------------------| -| State | abc xyz | Core | -| StandardState | abc xyz | Core | -| Conditions | abc xyz | Experimentalists, Experiment Runners, Theorists | -| Experiment Data | abc xyz | Experiment Runners, Theorists | -| Model | abc xyz | Theorists, Experimentalists | -| Variables | abc xyz | Experimentalists, Experiment Runners, Theorists | -| Components | abc xyz | Experimentalists, Experiment Runners, Theorists | -| Experimentalist | abc xyz | Experimentalists | -| Theorist | abc xyz | Theorists | -| Experiment Runner | abc xyz | Experiment Runners | -| Wrapper | abc xyz | Experimentalists, Experiment Runners, Theorists | -| Workflow | abc xyz | Experimentalists, Experiment Runners, Theorists | -| Cycle | abc xyz | Experimentalists, Experiment Runners, Theorists | -| Cylc | abc xyz | Experimentalists, Experiment Runners, Theorists | +| Term | Description | Relevant Modules | +|--------------------|---------------------------------------------------------------------------------------------------------------------------------------------|-------------------------------------------------| +| State | Base object that has all relevant fields and which uses the Delta mechanism to modify those fields. | Core | +| StandardState | An optional default State that has the following fields: variables, conditions, experiment_data, models. | Core | +| Variable | Definition of an experimental variable, including its name, type, units, allowed values, and range. | Experimentalists, Experiment Runners, Theorists | +| VariableCollection | Immutable metadata about dependent variables, independent variables, and covariates. | Experimentalists, Experiment Runners, Theorists | +| Conditions | A State field that defines what observations should be collected according to a specific combination of values of the independent variables | Experimentalists, Experiment Runners, Theorists | +| Experiment Data | abc xyz | Experiment Runners, Theorists | +| Model | abc xyz | Theorists, Experimentalists | +| Components | abc xyz | Experimentalists, Experiment Runners, Theorists | +| Experimentalist | abc xyz | Experimentalists | +| Theorist | abc xyz | Theorists | +| Experiment Runner | abc xyz | Experiment Runners | +| Wrapper | abc xyz | Experimentalists, Experiment Runners, Theorists | +| Workflow | abc xyz | Experimentalists, Experiment Runners, Theorists | +| Cycle | abc xyz | Experimentalists, Experiment Runners, Theorists | +| Cylc | abc xyz | Experimentalists, Experiment Runners, Theorists | From 40d7593da211c253180f748c220a831adfaa96d3 Mon Sep 17 00:00:00 2001 From: benwandrew Date: Wed, 18 Oct 2023 07:56:31 -0400 Subject: [PATCH 05/20] docs: finish descriptions of terms in terminology.md --- docs/terminology.md | 22 +++++++++++----------- 1 file changed, 11 insertions(+), 11 deletions(-) diff --git a/docs/terminology.md b/docs/terminology.md index 36cd65684..bd52c61f6 100644 --- a/docs/terminology.md +++ b/docs/terminology.md @@ -8,16 +8,16 @@ The following table includes naming conventions used throughout AutoRA. |--------------------|---------------------------------------------------------------------------------------------------------------------------------------------|-------------------------------------------------| | State | Base object that has all relevant fields and which uses the Delta mechanism to modify those fields. | Core | | StandardState | An optional default State that has the following fields: variables, conditions, experiment_data, models. | Core | -| Variable | Definition of an experimental variable, including its name, type, units, allowed values, and range. | Experimentalists, Experiment Runners, Theorists | +| Variables | A State field that holds experimental variables, which are defined according to name, type, units, allowed values, and range. | Experimentalists, Experiment Runners, Theorists | | VariableCollection | Immutable metadata about dependent variables, independent variables, and covariates. | Experimentalists, Experiment Runners, Theorists | | Conditions | A State field that defines what observations should be collected according to a specific combination of values of the independent variables | Experimentalists, Experiment Runners, Theorists | -| Experiment Data | abc xyz | Experiment Runners, Theorists | -| Model | abc xyz | Theorists, Experimentalists | -| Components | abc xyz | Experimentalists, Experiment Runners, Theorists | -| Experimentalist | abc xyz | Experimentalists | -| Theorist | abc xyz | Theorists | -| Experiment Runner | abc xyz | Experiment Runners | -| Wrapper | abc xyz | Experimentalists, Experiment Runners, Theorists | -| Workflow | abc xyz | Experimentalists, Experiment Runners, Theorists | -| Cycle | abc xyz | Experimentalists, Experiment Runners, Theorists | -| Cylc | abc xyz | Experimentalists, Experiment Runners, Theorists | +| Experiment Data | A State field that holds observations that correspond to the specified conditions. | Experiment Runners, Theorists | +| Model | A State field that holds the the collection of best fit equations produced by theorists. | Theorists, Experimentalists | +| Components | These are the distinct yet flexible capabilities of the AutoRA framework. | Experimentalists, Experiment Runners, Theorists | +| Experimentalist | A module that takes in models and outputs new conditions, which are intended to yield novel observations. | Experimentalists | +| Theorist | A module that takes in the full collection of conditions and observations and outputs equations that link the two (i.e., models) | Theorists | +| Experiment Runner | A module that takes in conditions and collects corresponding observations. | Experiment Runners | +| Wrapper | Special functions that make the components of AutoRA able to operate on State objects. | Experimentalists, Experiment Runners, Theorists | +| Workflow | A collection of tools that enable closed-loop empirical research with the AutoRA framework. | Experimentalists, Experiment Runners, Theorists | +| Cycle | A workflow tool that allows AutoRA components to be chained together in serial loop. | Experimentalists, Experiment Runners, Theorists | +| Cylc | A workflow engine for cycling systems that orchestrates distributed workflows of interdependent cycling tasks. | Experimentalists, Experiment Runners, Theorists | From 8d6ff9af534709c50d433933e24b606b2edf2e46 Mon Sep 17 00:00:00 2001 From: benwandrew Date: Wed, 18 Oct 2023 07:59:56 -0400 Subject: [PATCH 06/20] docs: get rid of floating empty brackets --- docs/terminology.md | 2 -- 1 file changed, 2 deletions(-) diff --git a/docs/terminology.md b/docs/terminology.md index bd52c61f6..0b5383bf9 100644 --- a/docs/terminology.md +++ b/docs/terminology.md @@ -2,8 +2,6 @@ The following table includes naming conventions used throughout AutoRA. -## [ ] - | Term | Description | Relevant Modules | |--------------------|---------------------------------------------------------------------------------------------------------------------------------------------|-------------------------------------------------| | State | Base object that has all relevant fields and which uses the Delta mechanism to modify those fields. | Core | From dd0d13335f99d4b4119276d8d5a5a1df8a088213 Mon Sep 17 00:00:00 2001 From: benwandrew Date: Wed, 18 Oct 2023 08:01:37 -0400 Subject: [PATCH 07/20] docs: typo --- docs/terminology.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/docs/terminology.md b/docs/terminology.md index 0b5383bf9..08e7f95a9 100644 --- a/docs/terminology.md +++ b/docs/terminology.md @@ -17,5 +17,5 @@ The following table includes naming conventions used throughout AutoRA. | Experiment Runner | A module that takes in conditions and collects corresponding observations. | Experiment Runners | | Wrapper | Special functions that make the components of AutoRA able to operate on State objects. | Experimentalists, Experiment Runners, Theorists | | Workflow | A collection of tools that enable closed-loop empirical research with the AutoRA framework. | Experimentalists, Experiment Runners, Theorists | -| Cycle | A workflow tool that allows AutoRA components to be chained together in serial loop. | Experimentalists, Experiment Runners, Theorists | +| Cycle | A workflow tool that allows AutoRA components to be chained together in serial loops. | Experimentalists, Experiment Runners, Theorists | | Cylc | A workflow engine for cycling systems that orchestrates distributed workflows of interdependent cycling tasks. | Experimentalists, Experiment Runners, Theorists | From 2aa68cd8083390830a149b257547c71dc0818806 Mon Sep 17 00:00:00 2001 From: benwandrew Date: Wed, 18 Oct 2023 08:02:28 -0400 Subject: [PATCH 08/20] docs: wording --- docs/terminology.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/docs/terminology.md b/docs/terminology.md index 08e7f95a9..b09fa2dbc 100644 --- a/docs/terminology.md +++ b/docs/terminology.md @@ -9,7 +9,7 @@ The following table includes naming conventions used throughout AutoRA. | Variables | A State field that holds experimental variables, which are defined according to name, type, units, allowed values, and range. | Experimentalists, Experiment Runners, Theorists | | VariableCollection | Immutable metadata about dependent variables, independent variables, and covariates. | Experimentalists, Experiment Runners, Theorists | | Conditions | A State field that defines what observations should be collected according to a specific combination of values of the independent variables | Experimentalists, Experiment Runners, Theorists | -| Experiment Data | A State field that holds observations that correspond to the specified conditions. | Experiment Runners, Theorists | +| Experiment Data | A State field that holds observations which correspond to the specified conditions. | Experiment Runners, Theorists | | Model | A State field that holds the the collection of best fit equations produced by theorists. | Theorists, Experimentalists | | Components | These are the distinct yet flexible capabilities of the AutoRA framework. | Experimentalists, Experiment Runners, Theorists | | Experimentalist | A module that takes in models and outputs new conditions, which are intended to yield novel observations. | Experimentalists | From fc5b0103ea0e9298894a7cab9804f96f7b2e3f21 Mon Sep 17 00:00:00 2001 From: benwandrew Date: Wed, 18 Oct 2023 08:03:25 -0400 Subject: [PATCH 09/20] docs: wording --- docs/terminology.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/docs/terminology.md b/docs/terminology.md index b09fa2dbc..ac66e2fec 100644 --- a/docs/terminology.md +++ b/docs/terminology.md @@ -11,7 +11,7 @@ The following table includes naming conventions used throughout AutoRA. | Conditions | A State field that defines what observations should be collected according to a specific combination of values of the independent variables | Experimentalists, Experiment Runners, Theorists | | Experiment Data | A State field that holds observations which correspond to the specified conditions. | Experiment Runners, Theorists | | Model | A State field that holds the the collection of best fit equations produced by theorists. | Theorists, Experimentalists | -| Components | These are the distinct yet flexible capabilities of the AutoRA framework. | Experimentalists, Experiment Runners, Theorists | +| Components | The distinct yet flexible capabilities of the AutoRA framework. | Experimentalists, Experiment Runners, Theorists | | Experimentalist | A module that takes in models and outputs new conditions, which are intended to yield novel observations. | Experimentalists | | Theorist | A module that takes in the full collection of conditions and observations and outputs equations that link the two (i.e., models) | Theorists | | Experiment Runner | A module that takes in conditions and collects corresponding observations. | Experiment Runners | From 1e34962069d3d4412466102ae152d1b0b60d5aa6 Mon Sep 17 00:00:00 2001 From: Ben Andrew Date: Fri, 20 Oct 2023 07:43:42 -0400 Subject: [PATCH 10/20] Update docs/terminology.md --- docs/terminology.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/docs/terminology.md b/docs/terminology.md index ac66e2fec..a2e01a092 100644 --- a/docs/terminology.md +++ b/docs/terminology.md @@ -9,7 +9,7 @@ The following table includes naming conventions used throughout AutoRA. | Variables | A State field that holds experimental variables, which are defined according to name, type, units, allowed values, and range. | Experimentalists, Experiment Runners, Theorists | | VariableCollection | Immutable metadata about dependent variables, independent variables, and covariates. | Experimentalists, Experiment Runners, Theorists | | Conditions | A State field that defines what observations should be collected according to a specific combination of values of the independent variables | Experimentalists, Experiment Runners, Theorists | -| Experiment Data | A State field that holds observations which correspond to the specified conditions. | Experiment Runners, Theorists | +| Experiment Data | A State field that holds specified conditions as well as the corresponding observations. | Experiment Runners, Theorists | | Model | A State field that holds the the collection of best fit equations produced by theorists. | Theorists, Experimentalists | | Components | The distinct yet flexible capabilities of the AutoRA framework. | Experimentalists, Experiment Runners, Theorists | | Experimentalist | A module that takes in models and outputs new conditions, which are intended to yield novel observations. | Experimentalists | From 44cf7dee26239d80ccb839ea9c00efc7931e7a86 Mon Sep 17 00:00:00 2001 From: Ben Andrew Date: Fri, 20 Oct 2023 07:45:57 -0400 Subject: [PATCH 11/20] Update docs/terminology.md --- docs/terminology.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/docs/terminology.md b/docs/terminology.md index a2e01a092..994c1dc21 100644 --- a/docs/terminology.md +++ b/docs/terminology.md @@ -11,7 +11,7 @@ The following table includes naming conventions used throughout AutoRA. | Conditions | A State field that defines what observations should be collected according to a specific combination of values of the independent variables | Experimentalists, Experiment Runners, Theorists | | Experiment Data | A State field that holds specified conditions as well as the corresponding observations. | Experiment Runners, Theorists | | Model | A State field that holds the the collection of best fit equations produced by theorists. | Theorists, Experimentalists | -| Components | The distinct yet flexible capabilities of the AutoRA framework. | Experimentalists, Experiment Runners, Theorists | +| Components | The objects that can act on the State (e.g., experimentalists, experiment runners, theorists). | Experimentalists, Experiment Runners, Theorists | | Experimentalist | A module that takes in models and outputs new conditions, which are intended to yield novel observations. | Experimentalists | | Theorist | A module that takes in the full collection of conditions and observations and outputs equations that link the two (i.e., models) | Theorists | | Experiment Runner | A module that takes in conditions and collects corresponding observations. | Experiment Runners | From 4cca60b7a4428192a30839c7b10611f50d179d58 Mon Sep 17 00:00:00 2001 From: Ben Andrew Date: Fri, 20 Oct 2023 07:49:27 -0400 Subject: [PATCH 12/20] Update docs/terminology.md --- docs/terminology.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/docs/terminology.md b/docs/terminology.md index 994c1dc21..9e584bb9e 100644 --- a/docs/terminology.md +++ b/docs/terminology.md @@ -12,7 +12,7 @@ The following table includes naming conventions used throughout AutoRA. | Experiment Data | A State field that holds specified conditions as well as the corresponding observations. | Experiment Runners, Theorists | | Model | A State field that holds the the collection of best fit equations produced by theorists. | Theorists, Experimentalists | | Components | The objects that can act on the State (e.g., experimentalists, experiment runners, theorists). | Experimentalists, Experiment Runners, Theorists | -| Experimentalist | A module that takes in models and outputs new conditions, which are intended to yield novel observations. | Experimentalists | +| Experimentalist | A component that outputs new conditions, which are intended to yield novel observations. | Experimentalists | | Theorist | A module that takes in the full collection of conditions and observations and outputs equations that link the two (i.e., models) | Theorists | | Experiment Runner | A module that takes in conditions and collects corresponding observations. | Experiment Runners | | Wrapper | Special functions that make the components of AutoRA able to operate on State objects. | Experimentalists, Experiment Runners, Theorists | From 457df8d8016f7f953eeac432f9cc4bdb2f860d4c Mon Sep 17 00:00:00 2001 From: Ben Andrew Date: Fri, 20 Oct 2023 07:50:15 -0400 Subject: [PATCH 13/20] Update docs/terminology.md --- docs/terminology.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/docs/terminology.md b/docs/terminology.md index 9e584bb9e..840a9ff5e 100644 --- a/docs/terminology.md +++ b/docs/terminology.md @@ -13,7 +13,7 @@ The following table includes naming conventions used throughout AutoRA. | Model | A State field that holds the the collection of best fit equations produced by theorists. | Theorists, Experimentalists | | Components | The objects that can act on the State (e.g., experimentalists, experiment runners, theorists). | Experimentalists, Experiment Runners, Theorists | | Experimentalist | A component that outputs new conditions, which are intended to yield novel observations. | Experimentalists | -| Theorist | A module that takes in the full collection of conditions and observations and outputs equations that link the two (i.e., models) | Theorists | +| Theorist | A component that takes in the full collection of conditions and observations and outputs models that link the two. | Theorists | | Experiment Runner | A module that takes in conditions and collects corresponding observations. | Experiment Runners | | Wrapper | Special functions that make the components of AutoRA able to operate on State objects. | Experimentalists, Experiment Runners, Theorists | | Workflow | A collection of tools that enable closed-loop empirical research with the AutoRA framework. | Experimentalists, Experiment Runners, Theorists | From c864f4d0719aaee3709e9e8c6a40a238604d5a22 Mon Sep 17 00:00:00 2001 From: Ben Andrew Date: Fri, 20 Oct 2023 07:50:46 -0400 Subject: [PATCH 14/20] Update docs/terminology.md --- docs/terminology.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/docs/terminology.md b/docs/terminology.md index 840a9ff5e..e266ace7b 100644 --- a/docs/terminology.md +++ b/docs/terminology.md @@ -14,7 +14,7 @@ The following table includes naming conventions used throughout AutoRA. | Components | The objects that can act on the State (e.g., experimentalists, experiment runners, theorists). | Experimentalists, Experiment Runners, Theorists | | Experimentalist | A component that outputs new conditions, which are intended to yield novel observations. | Experimentalists | | Theorist | A component that takes in the full collection of conditions and observations and outputs models that link the two. | Theorists | -| Experiment Runner | A module that takes in conditions and collects corresponding observations. | Experiment Runners | +| Experiment Runner | A component that takes in conditions and collects corresponding observations. | Experiment Runners | | Wrapper | Special functions that make the components of AutoRA able to operate on State objects. | Experimentalists, Experiment Runners, Theorists | | Workflow | A collection of tools that enable closed-loop empirical research with the AutoRA framework. | Experimentalists, Experiment Runners, Theorists | | Cycle | A workflow tool that allows AutoRA components to be chained together in serial loops. | Experimentalists, Experiment Runners, Theorists | From 056ae4f721126c6fb902cad1183d6efe36175c1a Mon Sep 17 00:00:00 2001 From: benwandrew Date: Fri, 20 Oct 2023 08:09:10 -0400 Subject: [PATCH 15/20] docs: add Delta to terminology.md --- docs/terminology.md | 11 ++++++----- 1 file changed, 6 insertions(+), 5 deletions(-) diff --git a/docs/terminology.md b/docs/terminology.md index e266ace7b..b4eabdd43 100644 --- a/docs/terminology.md +++ b/docs/terminology.md @@ -5,16 +5,17 @@ The following table includes naming conventions used throughout AutoRA. | Term | Description | Relevant Modules | |--------------------|---------------------------------------------------------------------------------------------------------------------------------------------|-------------------------------------------------| | State | Base object that has all relevant fields and which uses the Delta mechanism to modify those fields. | Core | +| Delta | An object that determines the extension behavior of State objects. | Core | | StandardState | An optional default State that has the following fields: variables, conditions, experiment_data, models. | Core | | Variables | A State field that holds experimental variables, which are defined according to name, type, units, allowed values, and range. | Experimentalists, Experiment Runners, Theorists | | VariableCollection | Immutable metadata about dependent variables, independent variables, and covariates. | Experimentalists, Experiment Runners, Theorists | | Conditions | A State field that defines what observations should be collected according to a specific combination of values of the independent variables | Experimentalists, Experiment Runners, Theorists | -| Experiment Data | A State field that holds specified conditions as well as the corresponding observations. | Experiment Runners, Theorists | +| Experiment Data | A State field that holds specified conditions as well as the corresponding observations. | Experiment Runners, Theorists | | Model | A State field that holds the the collection of best fit equations produced by theorists. | Theorists, Experimentalists | -| Components | The objects that can act on the State (e.g., experimentalists, experiment runners, theorists). | Experimentalists, Experiment Runners, Theorists | -| Experimentalist | A component that outputs new conditions, which are intended to yield novel observations. | Experimentalists | -| Theorist | A component that takes in the full collection of conditions and observations and outputs models that link the two. | Theorists | -| Experiment Runner | A component that takes in conditions and collects corresponding observations. | Experiment Runners | +| Components | The objects that can act on the State (e.g., experimentalists, experiment runners, theorists). | Experimentalists, Experiment Runners, Theorists | +| Experimentalist | A component that outputs new conditions, which are intended to yield novel observations. | Experimentalists | +| Theorist | A component that takes in the full collection of conditions and observations and outputs models that link the two. | Theorists | +| Experiment Runner | A component that takes in conditions and collects corresponding observations. | Experiment Runners | | Wrapper | Special functions that make the components of AutoRA able to operate on State objects. | Experimentalists, Experiment Runners, Theorists | | Workflow | A collection of tools that enable closed-loop empirical research with the AutoRA framework. | Experimentalists, Experiment Runners, Theorists | | Cycle | A workflow tool that allows AutoRA components to be chained together in serial loops. | Experimentalists, Experiment Runners, Theorists | From 156c53de640113d342ec6df3922e783ce4b551ee Mon Sep 17 00:00:00 2001 From: Ben Andrew Date: Wed, 25 Oct 2023 03:59:29 -0400 Subject: [PATCH 16/20] Update docs/terminology.md Co-authored-by: John Gerrard Holland --- docs/terminology.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/docs/terminology.md b/docs/terminology.md index b4eabdd43..701ffcee5 100644 --- a/docs/terminology.md +++ b/docs/terminology.md @@ -5,7 +5,7 @@ The following table includes naming conventions used throughout AutoRA. | Term | Description | Relevant Modules | |--------------------|---------------------------------------------------------------------------------------------------------------------------------------------|-------------------------------------------------| | State | Base object that has all relevant fields and which uses the Delta mechanism to modify those fields. | Core | -| Delta | An object that determines the extension behavior of State objects. | Core | +| Delta | An object with new data that can be added to a State, returning a new State which includes the new data. | Core | | StandardState | An optional default State that has the following fields: variables, conditions, experiment_data, models. | Core | | Variables | A State field that holds experimental variables, which are defined according to name, type, units, allowed values, and range. | Experimentalists, Experiment Runners, Theorists | | VariableCollection | Immutable metadata about dependent variables, independent variables, and covariates. | Experimentalists, Experiment Runners, Theorists | From 625dfa28a10cd024a98d9c65d90ad464ae14b8b2 Mon Sep 17 00:00:00 2001 From: Ben Andrew Date: Wed, 25 Oct 2023 03:59:50 -0400 Subject: [PATCH 17/20] Update docs/terminology.md Co-authored-by: John Gerrard Holland --- docs/terminology.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/docs/terminology.md b/docs/terminology.md index 701ffcee5..79bf25cdd 100644 --- a/docs/terminology.md +++ b/docs/terminology.md @@ -4,7 +4,7 @@ The following table includes naming conventions used throughout AutoRA. | Term | Description | Relevant Modules | |--------------------|---------------------------------------------------------------------------------------------------------------------------------------------|-------------------------------------------------| -| State | Base object that has all relevant fields and which uses the Delta mechanism to modify those fields. | Core | +| State | Object representing data from an experiment, like the conditions, observed experiment data and models. The State also includes rules on how to update those data if new data are provided using the "Delta mechanism". | Core | | Delta | An object with new data that can be added to a State, returning a new State which includes the new data. | Core | | StandardState | An optional default State that has the following fields: variables, conditions, experiment_data, models. | Core | | Variables | A State field that holds experimental variables, which are defined according to name, type, units, allowed values, and range. | Experimentalists, Experiment Runners, Theorists | From 8403b6a34b51654babee36309c88beddb322ec0e Mon Sep 17 00:00:00 2001 From: Ben Andrew Date: Wed, 25 Oct 2023 04:05:56 -0400 Subject: [PATCH 18/20] Update docs/terminology.md Co-authored-by: John Gerrard Holland --- docs/terminology.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/docs/terminology.md b/docs/terminology.md index 79bf25cdd..0204a6851 100644 --- a/docs/terminology.md +++ b/docs/terminology.md @@ -12,7 +12,7 @@ The following table includes naming conventions used throughout AutoRA. | Conditions | A State field that defines what observations should be collected according to a specific combination of values of the independent variables | Experimentalists, Experiment Runners, Theorists | | Experiment Data | A State field that holds specified conditions as well as the corresponding observations. | Experiment Runners, Theorists | | Model | A State field that holds the the collection of best fit equations produced by theorists. | Theorists, Experimentalists | -| Components | The objects that can act on the State (e.g., experimentalists, experiment runners, theorists). | Experimentalists, Experiment Runners, Theorists | +| Components | The functions that can act on the State (e.g., experimentalists, experiment runners, theorists). | Experimentalists, Experiment Runners, Theorists | | Experimentalist | A component that outputs new conditions, which are intended to yield novel observations. | Experimentalists | | Theorist | A component that takes in the full collection of conditions and observations and outputs models that link the two. | Theorists | | Experiment Runner | A component that takes in conditions and collects corresponding observations. | Experiment Runners | From 4316cd702c1c31471da22eec3c1c1ccb17d18c90 Mon Sep 17 00:00:00 2001 From: Ben Andrew Date: Thu, 26 Oct 2023 11:35:25 -0400 Subject: [PATCH 19/20] docs: remove cycle and cylc from terminology.md --- docs/terminology.md | 2 -- 1 file changed, 2 deletions(-) diff --git a/docs/terminology.md b/docs/terminology.md index 0204a6851..cb8c4889c 100644 --- a/docs/terminology.md +++ b/docs/terminology.md @@ -18,5 +18,3 @@ The following table includes naming conventions used throughout AutoRA. | Experiment Runner | A component that takes in conditions and collects corresponding observations. | Experiment Runners | | Wrapper | Special functions that make the components of AutoRA able to operate on State objects. | Experimentalists, Experiment Runners, Theorists | | Workflow | A collection of tools that enable closed-loop empirical research with the AutoRA framework. | Experimentalists, Experiment Runners, Theorists | -| Cycle | A workflow tool that allows AutoRA components to be chained together in serial loops. | Experimentalists, Experiment Runners, Theorists | -| Cylc | A workflow engine for cycling systems that orchestrates distributed workflows of interdependent cycling tasks. | Experimentalists, Experiment Runners, Theorists | From f6005621ecbbc67067af41adaab440c49a17a699 Mon Sep 17 00:00:00 2001 From: John Gerrard Holland Date: Thu, 26 Oct 2023 17:03:38 -0400 Subject: [PATCH 20/20] chore: reformat table --- docs/terminology.md | 32 ++++++++++++++++---------------- 1 file changed, 16 insertions(+), 16 deletions(-) diff --git a/docs/terminology.md b/docs/terminology.md index cb8c4889c..f64ac068c 100644 --- a/docs/terminology.md +++ b/docs/terminology.md @@ -2,19 +2,19 @@ The following table includes naming conventions used throughout AutoRA. -| Term | Description | Relevant Modules | -|--------------------|---------------------------------------------------------------------------------------------------------------------------------------------|-------------------------------------------------| -| State | Object representing data from an experiment, like the conditions, observed experiment data and models. The State also includes rules on how to update those data if new data are provided using the "Delta mechanism". | Core | -| Delta | An object with new data that can be added to a State, returning a new State which includes the new data. | Core | -| StandardState | An optional default State that has the following fields: variables, conditions, experiment_data, models. | Core | -| Variables | A State field that holds experimental variables, which are defined according to name, type, units, allowed values, and range. | Experimentalists, Experiment Runners, Theorists | -| VariableCollection | Immutable metadata about dependent variables, independent variables, and covariates. | Experimentalists, Experiment Runners, Theorists | -| Conditions | A State field that defines what observations should be collected according to a specific combination of values of the independent variables | Experimentalists, Experiment Runners, Theorists | -| Experiment Data | A State field that holds specified conditions as well as the corresponding observations. | Experiment Runners, Theorists | -| Model | A State field that holds the the collection of best fit equations produced by theorists. | Theorists, Experimentalists | -| Components | The functions that can act on the State (e.g., experimentalists, experiment runners, theorists). | Experimentalists, Experiment Runners, Theorists | -| Experimentalist | A component that outputs new conditions, which are intended to yield novel observations. | Experimentalists | -| Theorist | A component that takes in the full collection of conditions and observations and outputs models that link the two. | Theorists | -| Experiment Runner | A component that takes in conditions and collects corresponding observations. | Experiment Runners | -| Wrapper | Special functions that make the components of AutoRA able to operate on State objects. | Experimentalists, Experiment Runners, Theorists | -| Workflow | A collection of tools that enable closed-loop empirical research with the AutoRA framework. | Experimentalists, Experiment Runners, Theorists | +| Term | Description | Relevant Modules | +|--------------------|------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------|-------------------------------------------------| +| State | Object representing data from an experiment, like the conditions, observed experiment data and models. The State also includes rules on how to update those data if new data are provided using the "Delta mechanism". | Core | +| Delta | An object with new data that can be added to a State, returning a new State which includes the new data. | Core | +| StandardState | An optional default State that has the following fields: variables, conditions, experiment_data, models. | Core | +| Variables | A State field that holds experimental variables, which are defined according to name, type, units, allowed values, and range. | Experimentalists, Experiment Runners, Theorists | +| VariableCollection | Immutable metadata about dependent variables, independent variables, and covariates. | Experimentalists, Experiment Runners, Theorists | +| Conditions | A State field that defines what observations should be collected according to a specific combination of values of the independent variables | Experimentalists, Experiment Runners, Theorists | +| Experiment Data | A State field that holds specified conditions as well as the corresponding observations. | Experiment Runners, Theorists | +| Model | A State field that holds the the collection of best fit equations produced by theorists. | Theorists, Experimentalists | +| Components | The functions that can act on the State (e.g., experimentalists, experiment runners, theorists). | Experimentalists, Experiment Runners, Theorists | +| Experimentalist | A component that outputs new conditions, which are intended to yield novel observations. | Experimentalists | +| Theorist | A component that takes in the full collection of conditions and observations and outputs models that link the two. | Theorists | +| Experiment Runner | A component that takes in conditions and collects corresponding observations. | Experiment Runners | +| Wrapper | Special functions that make the components of AutoRA able to operate on State objects. | Experimentalists, Experiment Runners, Theorists | +| Workflow | A collection of tools that enable closed-loop empirical research with the AutoRA framework. | Experimentalists, Experiment Runners, Theorists |