Index
A
|
B
|
C
|
D
|
E
|
F
|
G
|
H
|
I
|
K
|
L
|
M
|
N
|
P
|
R
|
S
|
T
|
U
|
V
|
W
A
add_archive() (anadama2.workflow.Workflow method)
add_argument() (anadama2.workflow.Workflow method)
add_document() (anadama2.workflow.Workflow method)
add_task() (anadama2.grid.grid.Grid method)
(anadama2.workflow.Workflow method)
add_task_gridable() (anadama2.workflow.Workflow method)
add_task_group() (anadama2.workflow.Workflow method)
add_task_group_gridable() (anadama2.workflow.Workflow method)
add_worker() (anadama2.runners.GridRunner method)
allchildren() (in module anadama2.workflow)
allparents() (in module anadama2.workflow)
already_exists() (anadama2.workflow.Workflow method)
anadama2 (module)
anadama2.backends (module)
anadama2.document (module)
anadama2.grid.grid (module)
anadama2.grid.sge (module)
anadama2.grid.slurm (module)
anadama2.helpers (module)
anadama2.reporters (module)
anadama2.runners (module)
anadama2.tracked (module)
anadama2.util (module)
anadama2.workflow (module)
any_different() (in module anadama2.tracked)
apply_sh() (in module anadama2.helpers)
appropriate_lock() (anadama2.runners.ParallelLocalWorker static method)
appropriate_q_class() (anadama2.runners.ParallelLocalWorker static method)
auto() (in module anadama2.backends)
(in module anadama2.tracked)
B
Bag (class in anadama2.util)
Base (class in anadama2.tracked)
BaseBackend (class in anadama2.backends)
BaseReporter (class in anadama2.reporters)
BaseRunner (class in anadama2.runners)
C
capture() (in module anadama2.util)
cleanup() (anadama2.runners.GridRunner method)
(anadama2.runners.ParallelLocalRunner method)
close() (anadama2.backends.BaseBackend method)
(anadama2.backends.LevelDBBackend method)
compare() (anadama2.tracked.Base method)
(anadama2.tracked.Container method)
(anadama2.tracked.HugeTrackedFile method)
(anadama2.tracked.TrackedDirectory method)
(anadama2.tracked.TrackedExecutable method)
(anadama2.tracked.TrackedFile method)
(anadama2.tracked.TrackedFilePattern method)
(anadama2.tracked.TrackedFunction method)
(anadama2.tracked.TrackedString method)
(anadama2.tracked.TrackedVariable method)
compute_pcoa() (anadama2.document.PweaveDocument method)
ConsoleReporter (class in anadama2.reporters)
ConsoleReporter.stats (class in anadama2.reporters)
Container (class in anadama2.tracked)
create() (anadama2.backends.BaseBackend method)
(anadama2.backends.LevelDBBackend method)
(anadama2.document.PweaveDocument method)
(anadama2.util.Directory method)
current_grid_runner() (in module anadama2.runners)
D
default() (in module anadama2.backends)
(in module anadama2.reporters)
(in module anadama2.runners)
delete() (anadama2.backends.BaseBackend method)
(anadama2.backends.LevelDBBackend method)
delete_many() (anadama2.backends.BaseBackend method)
(anadama2.backends.LevelDBBackend method)
DependencyIndex (class in anadama2.tracked)
deserialize() (in module anadama2.util)
deserialize_csv() (in module anadama2.util)
deserialize_map_file() (in module anadama2.util)
dichotomize() (in module anadama2.util)
dict_to_cmd_opts() (in module anadama2.util)
dict_to_cmd_opts_iter() (in module anadama2.util)
Directory (class in anadama2.util)
discover_binaries() (in module anadama2.workflow)
discover_data_directory() (in module anadama2.backends)
do() (anadama2.grid.grid.Grid method)
(anadama2.workflow.Workflow method)
do_gridable() (anadama2.workflow.Workflow method)
Document (class in anadama2.document)
done (anadama2.reporters.ConsoleReporter.stats attribute)
(anadama2.reporters.VerboseConsoleReporter.stats attribute)
DryRunner (class in anadama2.runners)
E
evaluate_resource_requests() (anadama2.grid.grid.GridWorker static method)
exception_result() (in module anadama2.runners)
exists() (anadama2.backends.BaseBackend method)
(anadama2.backends.LevelDBBackend method)
(anadama2.tracked.Base method)
(anadama2.tracked.TrackedDirectory method)
(anadama2.tracked.TrackedExecutable method)
(anadama2.tracked.TrackedFile method)
(anadama2.tracked.TrackedFilePattern method)
(anadama2.util.Directory method)
F
fail (anadama2.reporters.ConsoleReporter.stats attribute)
(anadama2.reporters.VerboseConsoleReporter.stats attribute)
file_size() (in module anadama2.helpers)
files() (anadama2.util.Directory method)
filter_compressed() (in module anadama2.util)
filter_zero_columns() (anadama2.document.PweaveDocument method)
filter_zero_rows() (anadama2.document.PweaveDocument method)
find_on_path() (in module anadama2.util)
finished() (anadama2.reporters.BaseReporter method)
(anadama2.reporters.ConsoleReporter method)
(anadama2.reporters.LoggerReporter method)
(anadama2.reporters.ReporterGroup method)
(anadama2.reporters.VerboseConsoleReporter method)
first() (in module anadama2.util)
FORMAT (anadama2.reporters.LoggerReporter attribute)
format_command() (in module anadama2.helpers)
G
generator_flatten() (in module anadama2.util)
get_input_files() (anadama2.workflow.Workflow method)
get_name() (in module anadama2.util)
get_return_code() (anadama2.grid.grid.GridWorker static method)
get_vars() (anadama2.document.PweaveDocument method)
go() (anadama2.workflow.Workflow method)
Grid (class in anadama2.grid.grid)
grid_run (anadama2.reporters.VerboseConsoleReporter.stats attribute)
GridJobRequires (class in anadama2.grid.grid)
GridRunner (class in anadama2.runners)
GridWorker (class in anadama2.grid.grid)
guess_seq_filetype() (in module anadama2.util)
H
HasNoEqual (class in anadama2.util)
HugeTrackedFile (class in anadama2.tracked)
I
init() (anadama2.tracked.Base method)
(anadama2.tracked.TrackedExecutable method)
(anadama2.tracked.TrackedFile method)
(anadama2.tracked.TrackedFunction method)
(anadama2.tracked.TrackedString method)
(anadama2.tracked.TrackedVariable method)
intatleast1() (in module anadama2.util)
is_compressed() (in module anadama2.util)
islambda() (in module anadama2.util)
isnottask() (in module anadama2.util)
istask() (in module anadama2.util)
items() (anadama2.tracked.Container method)
K
kebab() (in module anadama2.util)
keepkeys() (in module anadama2.util)
key() (anadama2.tracked.Base static method)
(anadama2.tracked.Container static method)
(anadama2.tracked.TrackedExecutable static method)
(anadama2.tracked.TrackedFile static method)
(anadama2.tracked.TrackedFunction static method)
(anadama2.tracked.TrackedString static method)
(anadama2.tracked.TrackedVariable static method)
keyrename() (in module anadama2.util)
keys() (anadama2.backends.BaseBackend method)
(anadama2.backends.LevelDBBackend method)
L
LevelDBBackend (class in anadama2.backends)
link() (anadama2.tracked.DependencyIndex method)
log_event() (anadama2.reporters.LoggerReporter method)
log_grid_output() (anadama2.grid.grid.GridWorker static method)
LoggerReporter (class in anadama2.reporters)
lookup() (anadama2.backends.BaseBackend method)
(anadama2.backends.LevelDBBackend method)
lookup_many() (anadama2.backends.BaseBackend method)
(anadama2.backends.LevelDBBackend method)
M
max_message_length (anadama2.reporters.VerboseConsoleReporter.stats attribute)
memoized() (in module anadama2.util)
mkdirp() (in module anadama2.util)
msg_str (anadama2.reporters.ConsoleReporter attribute)
must_preexist (anadama2.tracked.Base attribute)
(anadama2.tracked.TrackedFunction attribute)
(anadama2.tracked.TrackedString attribute)
(anadama2.tracked.TrackedVariable attribute)
N
name_output_files() (anadama2.workflow.Workflow method)
noop() (in module anadama2.util)
P
ParallelLocalRunner (class in anadama2.runners)
ParallelLocalWorker (class in anadama2.runners)
parent_failed_result() (in module anadama2.runners)
parse_args() (anadama2.workflow.Workflow method)
parse_sh() (in module anadama2.helpers)
partition() (in module anadama2.util)
plot_barchart() (anadama2.document.PweaveDocument method)
plot_grouped_barchart() (anadama2.document.PweaveDocument method)
plot_scatter() (anadama2.document.PweaveDocument method)
plot_stacked_barchart() (anadama2.document.PweaveDocument method)
plot_stacked_barchart_grouped() (anadama2.document.PweaveDocument method)
PweaveDocument (class in anadama2.document)
R
read_log() (anadama2.reporters.LoggerReporter class method)
read_table() (anadama2.document.PweaveDocument method)
ready (anadama2.reporters.VerboseConsoleReporter.stats attribute)
ReporterGroup (class in anadama2.reporters)
reset() (anadama2.reporters.ConsoleReporter method)
(anadama2.reporters.VerboseConsoleReporter method)
rm() (in module anadama2.helpers)
rm_r() (in module anadama2.helpers)
route() (anadama2.runners.GridRunner method)
run() (anadama2.grid.grid.GridWorker method)
(anadama2.runners.ParallelLocalWorker method)
run_tasks() (anadama2.runners.BaseRunner method)
(anadama2.runners.DryRunner method)
(anadama2.runners.GridRunner method)
(anadama2.runners.ParallelLocalRunner method)
(anadama2.runners.SerialLocalRunner method)
RunFailed
S
save() (anadama2.backends.BaseBackend method)
(anadama2.backends.LevelDBBackend method)
serializable_attrs (anadama2.util.SerializableMixin attribute)
SerializableMixin (class in anadama2.util)
SerializationError
serialize() (in module anadama2.util)
serialize_map_file() (in module anadama2.util)
SerialLocalRunner (class in anadama2.runners)
SGE (class in anadama2.grid.sge)
sh() (in module anadama2.helpers)
(in module anadama2.util)
ShellException
show_hclust2() (anadama2.document.PweaveDocument method)
show_pcoa() (anadama2.document.PweaveDocument method)
show_pcoa_multiple_plots() (anadama2.document.PweaveDocument method)
show_table() (anadama2.document.PweaveDocument method)
skip (anadama2.reporters.ConsoleReporter.stats attribute)
(anadama2.reporters.VerboseConsoleReporter.stats attribute)
Slurm (class in anadama2.grid.slurm)
sorted_data_numerical_or_alphabetical() (anadama2.document.PweaveDocument method)
SparseMetadataException
start (anadama2.reporters.ConsoleReporter.stats attribute)
(anadama2.reporters.VerboseConsoleReporter.stats attribute)
started() (anadama2.reporters.BaseReporter method)
(anadama2.reporters.ConsoleReporter method)
(anadama2.reporters.LoggerReporter method)
(anadama2.reporters.ReporterGroup method)
(anadama2.reporters.VerboseConsoleReporter method)
sublist_template (anadama2.runners.DryRunner attribute)
sugar_list() (in module anadama2.util)
system() (in module anadama2.helpers)
T
take() (in module anadama2.util)
Task (class in anadama2)
task_command() (anadama2.reporters.BaseReporter method)
(anadama2.reporters.LoggerReporter method)
(anadama2.reporters.ReporterGroup method)
task_completed() (anadama2.reporters.BaseReporter method)
(anadama2.reporters.ConsoleReporter method)
(anadama2.reporters.LoggerReporter method)
(anadama2.reporters.ReporterGroup method)
(anadama2.reporters.VerboseConsoleReporter method)
task_failed() (anadama2.reporters.BaseReporter method)
(anadama2.reporters.ConsoleReporter method)
(anadama2.reporters.LoggerReporter method)
(anadama2.reporters.ReporterGroup method)
(anadama2.reporters.VerboseConsoleReporter method)
task_grid_status() (anadama2.reporters.BaseReporter method)
(anadama2.reporters.LoggerReporter method)
(anadama2.reporters.ReporterGroup method)
(anadama2.reporters.VerboseConsoleReporter method)
task_grid_status_polling() (anadama2.reporters.BaseReporter method)
(anadama2.reporters.LoggerReporter method)
(anadama2.reporters.ReporterGroup method)
(anadama2.reporters.VerboseConsoleReporter method)
task_results (anadama2.workflow.Workflow attribute)
task_running() (anadama2.reporters.BaseReporter method)
(anadama2.reporters.LoggerReporter method)
(anadama2.reporters.ReporterGroup method)
(anadama2.reporters.VerboseConsoleReporter method)
task_skipped() (anadama2.reporters.BaseReporter method)
(anadama2.reporters.ConsoleReporter method)
(anadama2.reporters.LoggerReporter method)
(anadama2.reporters.ReporterGroup method)
(anadama2.reporters.VerboseConsoleReporter method)
task_started() (anadama2.reporters.BaseReporter method)
(anadama2.reporters.ConsoleReporter method)
(anadama2.reporters.LoggerReporter method)
(anadama2.reporters.ReporterGroup method)
(anadama2.reporters.VerboseConsoleReporter method)
TaskFailed
TaskResult (class in anadama2.runners)
tasks (anadama2.workflow.Workflow attribute)
terminate() (anadama2.runners.GridRunner method)
(anadama2.runners.ParallelLocalRunner method)
TrackedDirectory (class in anadama2.tracked)
TrackedExecutable (class in anadama2.tracked)
TrackedFile (class in anadama2.tracked)
TrackedFilePattern (class in anadama2.tracked)
TrackedFunction (class in anadama2.tracked)
TrackedString (class in anadama2.tracked)
TrackedVariable (class in anadama2.tracked)
U
underscore() (in module anadama2.util)
V
VerboseConsoleReporter (class in anadama2.reporters)
VerboseConsoleReporter.stats (class in anadama2.reporters)
version() (anadama2.tracked.TrackedExecutable method)
W
WebhookReporter (class in anadama2.reporters)
which_compressed_idxs() (in module anadama2.util)
worker_run_loop() (in module anadama2.runners)
Workflow (anadama2.workflow attribute)
(class in anadama2.workflow)
write_table() (anadama2.document.PweaveDocument method)
anadama2
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