signac
v1.7.0
Go to Framework Documentation
Installation
Install with conda
Install with pip
Source Code Installation
Optional dependencies
Command Line Interface
clone
config
diff
document
export
find
import
index
init
job
move
project
rm
schema
shell
statepoint
sync
update-cache
view
API Reference
The Project
The JobsCursor class
The Job class
The Collection
The JSONDict
The H5Store
The H5StoreManager
Top-level functions
Submodules
signac.cite module
signac.sync module
signac.warnings module
signac.errors module
synced_collections package
Data Types
synced_collections.synced_collection module
synced_collections.synced_dict module
synced_collections.synced_list module
Backends
synced_collections.backends.collection_json module
synced_collections.backends.collection_mongodb module
synced_collections.backends.collection_redis module
synced_collections.backends.collection_zarr module
Buffers
synced_collections.buffers.buffered_collection module
synced_collections.buffers.file_buffered_collection module
synced_collections.buffers.serialized_file_buffered_collection module
synced_collections.buffers.memory_buffered_collection module
Miscellaneous Modules
synced_collections.utils module
synced_collections.validators module
Changelog
Version 1
[1.7.0] – 2021-06-08
Added
Changed
Deprecated
Fixed
[1.6.0] – 2021-01-24
Added
Changed
Deprecated
Fixed
[1.5.1] – 2020-12-19
Added
Changed
[1.5.0] – 2020-09-20
Added
Changed
Fixed
Deprecated
Removed
[1.4.0] – 2020-02-28
Added
Changed
Fixed
Removed
[1.3.0] – 2019-12-20
Added
Changed
Fixed
Deprecated
Removed
[1.2.0] – 2019-07-22
Added
Fixed
Deprecated
[1.1.0] – 2019-05-19
Added
Fixed
Removed
[1.0.0] – 2019-02-28
Added
Changed
Fixed
Removed
Version 0.9
[0.9.5] – 2019-01-31
Fixed
[0.9.4] – 2018-10-24
Added
Changed
Fixed
[0.9.3] – 2018-06-14
Added
Fixed
[0.9.2] – 2017-12-18
Added
Changed
Fixed
[0.9.1] – 2017-11-07
Fixed
[0.9.0] – 2017-10-28
Added
Changed
Version 0.8
[0.8.7] – 2017-10-05
Fixed
[0.8.6] – 2017-08-25
Fixed
[0.8.5] – 2017-06-07
Changed
Fixed
[0.8.4] – 2017-05-19
Added
Changed
[0.8.3] – 2017-05-10
Changed
Fixed
[0.8.2] – 2017-04-19
Fixed
[0.8.1] – 2017-04-17
Fixed
[0.8.0] – 2017-04-16
Added
Changed (breaking API)
Changed (non-breaking)
Deprecated
Fixed
Version 0.7
[0.7.1] – 2017-01-09
Added
Changed
Fixed
[0.7.0] – 2017-01-04
Added
Changed
Fixed
Removed
Version 0.6
[0.6.2] – 2017-12-15
Added
Removed
[0.6.1] – 2017-11-26
Changed
Fixed
[0.6.0] – 2016-11-18
Added
Changed
Removed
Fixed
Version 0.5
[0.5.0] – 2016-08-31
Added
Changed
Version 0.4
[0.4.0] – 2016-08-05
Added
Changed
Removed
Version 0.3
[0.3.0] – 2016-06-23
Added
Changed
Version 0.2
[0.2.9] – 2016-06-06
Added
Changed
Fixed
Deprecated
[0.2.8] – 2016-04-18
Added
Changed
[0.2.7] – 2016-02-29
Added
Changed
[0.2.6] – 2016-02-20
Added
Changed
Fixed
[0.2.5] – 2016-02-10
Added
Changed
Deprecated
Fixed
[0.2.4] – 2016-01-11
Added
Changed
Fixed
[0.2.3] – 2015-12-09
Fixed
[0.2.2] – 2015-11-30
Fixed
[0.2.1] – 2015-11-29
Added
[0.2.0] – 2015-11-05
Support and Development
Code contributions
Set up a development environment
The development workflow
Testing
Building documentation
Updating the changelog
signac
Docs
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Index
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Index
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A
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B
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C
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D
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E
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F
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G
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H
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I
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J
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K
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M
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N
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O
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P
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R
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S
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T
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U
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V
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W
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Z
_
_backend (signac.synced_collections.data_types.synced_collection.SyncedCollection attribute)
_flush() (signac.synced_collections.buffers.buffered_collection.BufferedCollection method)
_flush_buffer() (signac.synced_collections.buffers.buffered_collection.BufferedCollection class method)
_from_base() (signac.synced_collections.data_types.synced_collection.SyncedCollection class method)
_is_buffered (signac.synced_collections.buffers.buffered_collection.BufferedCollection attribute)
_load() (signac.synced_collections.buffers.buffered_collection.BufferedCollection method)
(signac.synced_collections.data_types.synced_collection.SyncedCollection method)
_load_from_buffer() (signac.synced_collections.buffers.buffered_collection.BufferedCollection method)
_load_from_resource() (signac.synced_collections.data_types.synced_collection.SyncedCollection method)
_LoadAndSave (class in signac.synced_collections.data_types.synced_collection)
_LoadSaveType (signac.synced_collections.data_types.synced_collection.SyncedCollection attribute)
_register_validators() (signac.synced_collections.data_types.synced_collection.SyncedCollection class method)
_save() (signac.synced_collections.buffers.buffered_collection.BufferedCollection method)
(signac.synced_collections.data_types.synced_collection.SyncedCollection method)
_save_to_buffer() (signac.synced_collections.buffers.buffered_collection.BufferedCollection method)
_save_to_resource() (signac.synced_collections.data_types.synced_collection.SyncedCollection method)
_to_base() (signac.synced_collections.data_types.synced_collection.SyncedCollection method)
_update() (signac.synced_collections.data_types.synced_collection.SyncedCollection method)
_validate() (signac.synced_collections.data_types.synced_collection.SyncedCollection method)
A
abstract_type_identifiers (signac.synced_collections.utils.AbstractTypeResolver attribute)
AbstractTypeResolver (class in signac.synced_collections.utils)
always() (signac.sync.FileSync static method)
append() (signac.synced_collections.data_types.synced_list.SyncedList method)
AuthenticationError
B
backend_is_buffered() (signac.synced_collections.buffers.buffered_collection.BufferedCollection class method)
bibtex() (in module signac.cite)
buffer_backend() (signac.synced_collections.buffers.buffered_collection.BufferedCollection class method)
(signac.synced_collections.buffers.file_buffered_collection.FileBufferedCollection class method)
BufferedCollection (class in signac.synced_collections.buffers.buffered_collection)
BufferedFileError
BufferedJSONAttrDict (class in signac.synced_collections.backends.collection_json)
BufferedJSONAttrList (class in signac.synced_collections.backends.collection_json)
BufferedJSONCollection (class in signac.synced_collections.backends.collection_json)
BufferedJSONDict (class in signac.synced_collections.backends.collection_json)
BufferedJSONList (class in signac.synced_collections.backends.collection_json)
BufferException
build_job_search_index() (signac.Project method)
build_job_statepoint_index() (signac.Project method)
C
check() (signac.Project method)
clear() (signac.Collection method)
(signac.H5Store method)
(signac.contrib.job.Job method)
(signac.synced_collections.data_types.synced_dict.SyncedDict method)
(signac.synced_collections.data_types.synced_list.SyncedList method)
client (signac.synced_collections.backends.collection_redis.RedisCollection attribute)
clone() (signac.Project method)
close() (signac.Collection method)
(signac.H5Store method)
(signac.contrib.job.Job method)
cls (signac.H5StoreManager attribute)
codec (signac.synced_collections.backends.collection_zarr.ZarrCollection attribute)
Collection (class in signac)
collection (signac.synced_collections.backends.collection_mongodb.MongoDBCollection attribute)
config (signac.Project attribute)
ConfigError
COPY (signac.sync.DocSync attribute)
create_access_module() (signac.Project method)
create_linked_view() (signac.Project method)
D
data (signac.contrib.job.Job attribute)
(signac.Project attribute)
default() (in module signac.synced_collections.utils)
(signac.synced_collections.utils.SyncedCollectionJSONEncoder method)
delete_many() (signac.Collection method)
delete_one() (signac.Collection method)
DestinationExistsError
detect_schema() (signac.Project method)
diff_jobs() (in module signac)
disable_multithreading() (signac.synced_collections.buffers.file_buffered_collection.FileBufferedCollection class method)
(signac.synced_collections.data_types.synced_collection.SyncedCollection class method)
doc (signac.contrib.job.Job attribute)
(signac.Project attribute)
DocSync (class in signac.sync)
DocSync.ByKey (class in signac.sync)
document (signac.contrib.job.Job attribute)
(signac.Project attribute)
DocumentSyncConflict
dump() (signac.Collection method)
dump_statepoints() (signac.Project method)
E
enable_multithreading() (signac.synced_collections.buffers.file_buffered_collection.FileBufferedCollection class method)
(signac.synced_collections.data_types.synced_collection.SyncedCollection class method)
Error
export() (in module signac)
export_one() (in module signac)
export_pymongo() (in module signac)
export_to() (signac.contrib.project.JobsCursor method)
(signac.Project method)
export_to_mirror() (in module signac)
ExportError
extend() (signac.synced_collections.data_types.synced_list.SyncedList method)
F
fetch() (in module signac)
FetchError
file (signac.H5Store attribute)
FileBufferedCollection (class in signac.synced_collections.buffers.file_buffered_collection)
filename (signac.errors.FileSyncConflict attribute)
(signac.H5Store attribute)
(signac.synced_collections.backends.collection_json.JSONCollection attribute)
files (signac.errors.BufferedFileError attribute)
FileSync (class in signac.sync)
FileSync.Ask (class in signac.sync)
FileSyncConflict
find() (signac.Collection method)
find_job_ids() (signac.Project method)
find_jobs() (signac.Project method)
find_one() (signac.Collection method)
flush() (in module signac)
(signac.Collection method)
(signac.H5Store method)
fn() (signac.contrib.job.Job method)
(signac.Project method)
FN_CACHE (signac.Project attribute)
FN_DOCUMENT (signac.contrib.job.Job attribute)
(signac.Project attribute)
FN_MANIFEST (signac.contrib.job.Job attribute)
FN_STATEPOINTS (signac.Project attribute)
G
get() (signac.H5Store method)
(signac.synced_collections.data_types.synced_dict.SyncedDict method)
get_buffer_capacity() (signac.synced_collections.buffers.file_buffered_collection.FileBufferedCollection class method)
get_current_buffer_size() (signac.synced_collections.buffers.file_buffered_collection.FileBufferedCollection class method)
get_database() (in module signac)
get_id() (signac.contrib.job.Job method)
(signac.Project method)
get_job() (in module signac)
(signac.Project class method)
get_project() (in module signac)
(signac.Project class method)
get_statepoint() (signac.Project method)
get_type() (signac.synced_collections.utils.AbstractTypeResolver method)
group (signac.synced_collections.backends.collection_zarr.ZarrCollection attribute)
groupby() (signac.contrib.project.JobsCursor method)
(signac.Project method)
groupbydoc() (signac.contrib.project.JobsCursor method)
(signac.Project method)
H
H5Store (class in signac)
H5StoreManager (class in signac)
HDF5 integration
I
id (signac.contrib.job.Job attribute)
(signac.Project attribute)
ids (signac.Collection attribute)
import_from() (signac.Project method)
IncompatibleSchemaVersion
index() (in module signac)
(signac.Collection method)
(signac.Project method)
index_files() (in module signac)
init() (signac.contrib.job.Job method)
init_project() (in module signac)
(signac.Project class method)
insert() (signac.synced_collections.data_types.synced_list.SyncedList method)
insert_one() (signac.Collection method)
InvalidKeyError
is_base_type() (signac.synced_collections.data_types.synced_collection.SyncedCollection class method)
(signac.synced_collections.data_types.synced_dict.SyncedDict class method)
(signac.synced_collections.data_types.synced_list.SyncedList class method)
isfile() (signac.contrib.job.Job method)
(signac.Project method)
items() (signac.H5Store method)
(signac.synced_collections.data_types.synced_dict.SyncedDict method)
J
Job (class in signac.contrib.job)
JobsCorruptedError
JobsCursor (class in signac.contrib.project)
json_attr_dict_validator() (in module signac.synced_collections.backends.collection_json)
json_format_validator() (in module signac.synced_collections.validators)
JSONAttrDict (class in signac.synced_collections.backends.collection_json)
JSONAttrList (class in signac.synced_collections.backends.collection_json)
JSONCollection (class in signac.synced_collections.backends.collection_json)
JSONDict (class in signac.synced_collections.backends.collection_json)
(in module signac)
JSONList (class in signac.synced_collections.backends.collection_json)
K
key (signac.synced_collections.backends.collection_redis.RedisCollection attribute)
KEY_DATA (signac.contrib.job.Job attribute)
(signac.Project attribute)
keys (signac.errors.DocumentSyncConflict attribute)
keys() (signac.H5Store method)
(signac.H5StoreManager method)
(signac.sync.FileSync class method)
(signac.synced_collections.data_types.synced_dict.SyncedDict method)
KeyTypeError
M
main() (signac.Collection method)
MemoryBufferedJSONAttrDict (class in signac.synced_collections.backends.collection_json)
MemoryBufferedJSONAttrList (class in signac.synced_collections.backends.collection_json)
MemoryBufferedJSONCollection (class in signac.synced_collections.backends.collection_json)
MemoryBufferedJSONDict (class in signac.synced_collections.backends.collection_json)
MemoryBufferedJSONList (class in signac.synced_collections.backends.collection_json)
min_len_unique_id() (signac.Project method)
mode (signac.H5Store attribute)
MongoDB database backend
MongoDBCollection (class in signac.synced_collections.backends.collection_mongodb)
MongoDBDict (class in signac.synced_collections.backends.collection_mongodb)
MongoDBList (class in signac.synced_collections.backends.collection_mongodb)
move() (signac.contrib.job.Job method)
N
name (signac.synced_collections.backends.collection_zarr.ZarrCollection attribute)
never() (signac.sync.FileSync static method)
next() (signac.contrib.project.JobsCursor method)
no_dot_in_key() (in module signac.synced_collections.validators)
NO_SYNC (signac.sync.DocSync attribute)
num_jobs() (signac.Project method)
O
open() (signac.Collection class method)
(signac.H5Store method)
(signac.contrib.job.Job method)
open_job() (signac.Project method)
P
pop() (signac.H5Store method)
(signac.synced_collections.data_types.synced_dict.SyncedDict method)
popitem() (signac.H5Store method)
(signac.synced_collections.data_types.synced_dict.SyncedDict method)
prefix (signac.H5StoreManager attribute)
primary_key (signac.Collection attribute)
Project (class in signac)
R
read_json() (signac.Collection class method)
read_statepoints() (signac.Project method)
RedisCollection (class in signac.synced_collections.backends.collection_redis)
RedisDict (class in signac.synced_collections.backends.collection_redis)
RedisList (class in signac.synced_collections.backends.collection_redis)
reference() (in module signac.cite)
remove() (signac.contrib.job.Job method)
(signac.synced_collections.data_types.synced_list.SyncedList method)
repair() (signac.Project method)
replace_one() (signac.Collection method)
require_string_key() (in module signac.synced_collections.validators)
reset() (signac.contrib.job.Job method)
(signac.synced_collections.data_types.synced_dict.SyncedDict method)
(signac.synced_collections.data_types.synced_list.SyncedList method)
reset_statepoint() (signac.contrib.job.Job method)
(signac.Project method)
root_directory() (signac.Project method)
S
SchemaSyncConflict
SerializedFileBufferedCollection (class in signac.synced_collections.buffers.serialized_file_buffered_collection)
set_buffer_capacity() (signac.synced_collections.buffers.file_buffered_collection.FileBufferedCollection class method)
setdefault() (signac.H5Store method)
(signac.synced_collections.data_types.synced_dict.SyncedDict method)
SharedMemoryFileBufferedCollection (class in signac.synced_collections.buffers.memory_buffered_collection)
signac (module)
signac.cite (module)
signac.errors (module)
signac.sync (module)
signac.synced_collections.backends.collection_json (module)
signac.synced_collections.backends.collection_mongodb (module)
signac.synced_collections.backends.collection_redis (module)
signac.synced_collections.backends.collection_zarr (module)
signac.synced_collections.buffers.buffered_collection (module)
signac.synced_collections.buffers.file_buffered_collection (module)
signac.synced_collections.buffers.memory_buffered_collection (module)
signac.synced_collections.buffers.serialized_file_buffered_collection (module)
signac.synced_collections.data_types.synced_collection (module)
signac.synced_collections.data_types.synced_dict (module)
signac.synced_collections.data_types.synced_list (module)
signac.synced_collections.utils (module)
signac.synced_collections.validators (module)
signac.warnings (module)
SignacDeprecationWarning
sp (signac.contrib.job.Job attribute)
statepoint (signac.contrib.job.Job attribute)
StatepointParsingError
stores (signac.contrib.job.Job attribute)
(signac.Project attribute)
sync() (signac.contrib.job.Job method)
(signac.Project method)
sync_jobs() (in module signac.sync)
sync_projects() (in module signac.sync)
SyncConflict
SyncedCollection (class in signac.synced_collections.data_types.synced_collection)
SyncedCollectionJSONEncoder (class in signac.synced_collections.utils)
SyncedDict (class in signac.synced_collections.data_types.synced_dict)
SyncedList (class in signac.synced_collections.data_types.synced_list)
T
temporary_project() (signac.Project method)
TemporaryProject() (in module signac)
to_dataframe() (signac.contrib.project.JobsCursor method)
(signac.Project method)
to_json() (signac.Collection method)
type_map (signac.synced_collections.utils.AbstractTypeResolver attribute)
U
uid (signac.synced_collections.backends.collection_mongodb.MongoDBCollection attribute)
update() (signac.Collection method)
(signac.H5Store method)
(signac.sync.DocSync static method)
(signac.sync.FileSync static method)
(signac.synced_collections.data_types.synced_dict.SyncedDict method)
update_cache() (signac.Project method)
update_statepoint() (signac.contrib.job.Job method)
(signac.Project method)
V
values() (signac.H5Store method)
(signac.synced_collections.data_types.synced_dict.SyncedDict method)
W
workspace() (signac.contrib.job.Job method)
(signac.Project method)
WorkspaceError
write_statepoints() (signac.Project method)
ws (signac.contrib.job.Job attribute)
Z
ZarrCollection (class in signac.synced_collections.backends.collection_zarr)
ZarrDict (class in signac.synced_collections.backends.collection_zarr)
ZarrList (class in signac.synced_collections.backends.collection_zarr)
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