Closed gwaybio closed 3 years ago
In step 2, I ran into a new bug:
[NbConvertApp] Converting notebook 1.merge-datasets-gct.ipynb to html [NbConvertApp] Writing 600777 bytes to scripts/html/1.merge-datasets-gct.html [NbConvertApp] Converting notebook 2.umap-aggregate-profiles.ipynb to html Traceback (most recent call last): File "/Users/gway/miniconda3/envs/resistance-mechanisms/bin/jupyter-nbconvert", line 11, in <module> sys.exit(main()) File "/Users/gway/miniconda3/envs/resistance-mechanisms/lib/python3.7/site-packages/jupyter_core/application.py", line 254, in launch_instance return super(JupyterApp, cls).launch_instance(argv=argv, **kwargs) File "/Users/gway/miniconda3/envs/resistance-mechanisms/lib/python3.7/site-packages/traitlets/config/application.py", line 845, in launch_instance app.start() File "/Users/gway/miniconda3/envs/resistance-mechanisms/lib/python3.7/site-packages/nbconvert/nbconvertapp.py", line 350, in start self.convert_notebooks() File "/Users/gway/miniconda3/envs/resistance-mechanisms/lib/python3.7/site-packages/nbconvert/nbconvertapp.py", line 524, in convert_notebooks self.convert_single_notebook(notebook_filename) File "/Users/gway/miniconda3/envs/resistance-mechanisms/lib/python3.7/site-packages/nbconvert/nbconvertapp.py", line 489, in convert_single_notebook output, resources = self.export_single_notebook(notebook_filename, resources, input_buffer=input_buffer) File "/Users/gway/miniconda3/envs/resistance-mechanisms/lib/python3.7/site-packages/nbconvert/nbconvertapp.py", line 418, in export_single_notebook output, resources = self.exporter.from_filename(notebook_filename, resources=resources) File "/Users/gway/miniconda3/envs/resistance-mechanisms/lib/python3.7/site-packages/nbconvert/exporters/exporter.py", line 181, in from_filename return self.from_file(f, resources=resources, **kw) File "/Users/gway/miniconda3/envs/resistance-mechanisms/lib/python3.7/site-packages/nbconvert/exporters/exporter.py", line 199, in from_file return self.from_notebook_node(nbformat.read(file_stream, as_version=4), resources=resources, **kw) File "/Users/gway/miniconda3/envs/resistance-mechanisms/lib/python3.7/site-packages/nbconvert/exporters/html.py", line 119, in from_notebook_node return super().from_notebook_node(nb, resources, **kw) File "/Users/gway/miniconda3/envs/resistance-mechanisms/lib/python3.7/site-packages/nbconvert/exporters/templateexporter.py", line 369, in from_notebook_node nb_copy, resources = super().from_notebook_node(nb, resources, **kw) File "/Users/gway/miniconda3/envs/resistance-mechanisms/lib/python3.7/site-packages/nbconvert/exporters/exporter.py", line 143, in from_notebook_node nb_copy, resources = self._preprocess(nb_copy, resources) File "/Users/gway/miniconda3/envs/resistance-mechanisms/lib/python3.7/site-packages/nbconvert/exporters/exporter.py", line 318, in _preprocess nbc, resc = preprocessor(nbc, resc) File "/Users/gway/miniconda3/envs/resistance-mechanisms/lib/python3.7/site-packages/nbconvert/preprocessors/base.py", line 47, in __call__ return self.preprocess(nb, resources) File "/Users/gway/miniconda3/envs/resistance-mechanisms/lib/python3.7/site-packages/nbconvert/preprocessors/execute.py", line 79, in preprocess self.execute() File "/Users/gway/miniconda3/envs/resistance-mechanisms/lib/python3.7/site-packages/nbclient/util.py", line 74, in wrapped return just_run(coro(*args, **kwargs)) File "/Users/gway/miniconda3/envs/resistance-mechanisms/lib/python3.7/site-packages/nbclient/util.py", line 53, in just_run return loop.run_until_complete(coro) File "/Users/gway/miniconda3/envs/resistance-mechanisms/lib/python3.7/asyncio/base_events.py", line 573, in run_until_complete return future.result() File "/Users/gway/miniconda3/envs/resistance-mechanisms/lib/python3.7/site-packages/nbclient/client.py", line 554, in async_execute cell, index, execution_count=self.code_cells_executed + 1 File "/Users/gway/miniconda3/envs/resistance-mechanisms/lib/python3.7/site-packages/nbconvert/preprocessors/execute.py", line 123, in async_execute_cell cell, resources = self.preprocess_cell(cell, self.resources, cell_index) File "/Users/gway/miniconda3/envs/resistance-mechanisms/lib/python3.7/site-packages/nbconvert/preprocessors/execute.py", line 146, in preprocess_cell cell = run_sync(NotebookClient.async_execute_cell)(self, cell, index, store_history=self.store_history) File "/Users/gway/miniconda3/envs/resistance-mechanisms/lib/python3.7/site-packages/nbclient/util.py", line 74, in wrapped return just_run(coro(*args, **kwargs)) File "/Users/gway/miniconda3/envs/resistance-mechanisms/lib/python3.7/site-packages/nbclient/util.py", line 53, in just_run return loop.run_until_complete(coro) File "/Users/gway/miniconda3/envs/resistance-mechanisms/lib/python3.7/site-packages/nest_asyncio.py", line 70, in run_until_complete return f.result() File "/Users/gway/miniconda3/envs/resistance-mechanisms/lib/python3.7/asyncio/futures.py", line 178, in result raise self._exception File "/Users/gway/miniconda3/envs/resistance-mechanisms/lib/python3.7/asyncio/tasks.py", line 223, in __step result = coro.send(None) File "/Users/gway/miniconda3/envs/resistance-mechanisms/lib/python3.7/site-packages/nbclient/client.py", line 857, in async_execute_cell self._check_raise_for_error(cell, exec_reply) File "/Users/gway/miniconda3/envs/resistance-mechanisms/lib/python3.7/site-packages/nbclient/client.py", line 760, in _check_raise_for_error raise CellExecutionError.from_cell_and_msg(cell, exec_reply_content) nbclient.exceptions.CellExecutionError: An error occurred while executing the following cell: ------------------ import os import numpy as np import pandas as pd import umap import plotnine as gg from pycytominer import feature_select from pycytominer.cyto_utils import infer_cp_features ------------------ --------------------------------------------------------------------------- AssertionError Traceback (most recent call last) ~/miniconda3/envs/resistance-mechanisms/lib/python3.7/site-packages/numba/core/errors.py in new_error_context(fmt_, *args, **kwargs) 743 try: --> 744 yield 745 except NumbaError as e: ~/miniconda3/envs/resistance-mechanisms/lib/python3.7/site-packages/numba/core/lowering.py in lower_block(self, block) 229 loc=self.loc, errcls_=defaulterrcls): --> 230 self.lower_inst(inst) 231 self.post_block(block) ~/miniconda3/envs/resistance-mechanisms/lib/python3.7/site-packages/numba/core/lowering.py in lower_inst(self, inst) 327 val = self.lower_assign(ty, inst) --> 328 self.storevar(val, inst.target.name) 329 ~/miniconda3/envs/resistance-mechanisms/lib/python3.7/site-packages/numba/core/lowering.py in storevar(self, value, name) 1277 name=name) -> 1278 raise AssertionError(msg) 1279 AssertionError: Storing i64 to ptr of i32 ('dim'). FE type int32 During handling of the above exception, another exception occurred: LoweringError Traceback (most recent call last) <ipython-input-1-886110eebc29> in <module> 2 import numpy as np 3 import pandas as pd ----> 4 import umap 5 6 import plotnine as gg ~/miniconda3/envs/resistance-mechanisms/lib/python3.7/site-packages/umap/__init__.py in <module> ----> 1 from .umap_ import UMAP 2 3 # Workaround: https://github.com/numba/numba/issues/3341 4 import numba 5 ~/miniconda3/envs/resistance-mechanisms/lib/python3.7/site-packages/umap/umap_.py in <module> 52 from umap.spectral import spectral_layout 53 from umap.utils import deheap_sort, submatrix ---> 54 from umap.layouts import ( 55 optimize_layout_euclidean, 56 optimize_layout_generic, ~/miniconda3/envs/resistance-mechanisms/lib/python3.7/site-packages/umap/layouts.py in <module> 34 "result": numba.types.float32, 35 "diff": numba.types.float32, ---> 36 "dim": numba.types.int32, 37 }, 38 ) ~/miniconda3/envs/resistance-mechanisms/lib/python3.7/site-packages/numba/core/decorators.py in wrapper(func) 219 with typeinfer.register_dispatcher(disp): 220 for sig in sigs: --> 221 disp.compile(sig) 222 disp.disable_compile() 223 return disp ~/miniconda3/envs/resistance-mechanisms/lib/python3.7/site-packages/numba/core/dispatcher.py in compile(self, sig) 907 with ev.trigger_event("numba:compile", data=ev_details): 908 try: --> 909 cres = self._compiler.compile(args, return_type) 910 except errors.ForceLiteralArg as e: 911 def folded(args, kws): ~/miniconda3/envs/resistance-mechanisms/lib/python3.7/site-packages/numba/core/dispatcher.py in compile(self, args, return_type) 77 78 def compile(self, args, return_type): ---> 79 status, retval = self._compile_cached(args, return_type) 80 if status: 81 return retval ~/miniconda3/envs/resistance-mechanisms/lib/python3.7/site-packages/numba/core/dispatcher.py in _compile_cached(self, args, return_type) 91 92 try: ---> 93 retval = self._compile_core(args, return_type) 94 except errors.TypingError as e: 95 self._failed_cache[key] = e ~/miniconda3/envs/resistance-mechanisms/lib/python3.7/site-packages/numba/core/dispatcher.py in _compile_core(self, args, return_type) 109 args=args, return_type=return_type, 110 flags=flags, locals=self.locals, --> 111 pipeline_class=self.pipeline_class) 112 # Check typing error if object mode is used 113 if cres.typing_error is not None and not flags.enable_pyobject: ~/miniconda3/envs/resistance-mechanisms/lib/python3.7/site-packages/numba/core/compiler.py in compile_extra(typingctx, targetctx, func, args, return_type, flags, locals, library, pipeline_class) 604 pipeline = pipeline_class(typingctx, targetctx, library, 605 args, return_type, flags, locals) --> 606 return pipeline.compile_extra(func) 607 608 ~/miniconda3/envs/resistance-mechanisms/lib/python3.7/site-packages/numba/core/compiler.py in compile_extra(self, func) 351 self.state.lifted = () 352 self.state.lifted_from = None --> 353 return self._compile_bytecode() 354 355 def compile_ir(self, func_ir, lifted=(), lifted_from=None): ~/miniconda3/envs/resistance-mechanisms/lib/python3.7/site-packages/numba/core/compiler.py in _compile_bytecode(self) 413 """ 414 assert self.state.func_ir is None --> 415 return self._compile_core() 416 417 def _compile_ir(self): ~/miniconda3/envs/resistance-mechanisms/lib/python3.7/site-packages/numba/core/compiler.py in _compile_core(self) 393 self.state.status.fail_reason = e 394 if is_final_pipeline: --> 395 raise e 396 else: 397 raise CompilerError("All available pipelines exhausted") ~/miniconda3/envs/resistance-mechanisms/lib/python3.7/site-packages/numba/core/compiler.py in _compile_core(self) 384 res = None 385 try: --> 386 pm.run(self.state) 387 if self.state.cr is not None: 388 break ~/miniconda3/envs/resistance-mechanisms/lib/python3.7/site-packages/numba/core/compiler_machinery.py in run(self, state) 337 (self.pipeline_name, pass_desc) 338 patched_exception = self._patch_error(msg, e) --> 339 raise patched_exception 340 341 def dependency_analysis(self): ~/miniconda3/envs/resistance-mechanisms/lib/python3.7/site-packages/numba/core/compiler_machinery.py in run(self, state) 328 pass_inst = _pass_registry.get(pss).pass_inst 329 if isinstance(pass_inst, CompilerPass): --> 330 self._runPass(idx, pass_inst, state) 331 else: 332 raise BaseException("Legacy pass in use") ~/miniconda3/envs/resistance-mechanisms/lib/python3.7/site-packages/numba/core/compiler_lock.py in _acquire_compile_lock(*args, **kwargs) 33 def _acquire_compile_lock(*args, **kwargs): 34 with self: ---> 35 return func(*args, **kwargs) 36 return _acquire_compile_lock 37 ~/miniconda3/envs/resistance-mechanisms/lib/python3.7/site-packages/numba/core/compiler_machinery.py in _runPass(self, index, pss, internal_state) 287 mutated |= check(pss.run_initialization, internal_state) 288 with SimpleTimer() as pass_time: --> 289 mutated |= check(pss.run_pass, internal_state) 290 with SimpleTimer() as finalize_time: 291 mutated |= check(pss.run_finalizer, internal_state) ~/miniconda3/envs/resistance-mechanisms/lib/python3.7/site-packages/numba/core/compiler_machinery.py in check(func, compiler_state) 260 261 def check(func, compiler_state): --> 262 mangled = func(compiler_state) 263 if mangled not in (True, False): 264 msg = ("CompilerPass implementations should return True/False. " ~/miniconda3/envs/resistance-mechanisms/lib/python3.7/site-packages/numba/core/typed_passes.py in run_pass(self, state) 461 462 # TODO: Pull this out into the pipeline --> 463 NativeLowering().run_pass(state) 464 lowered = state['cr'] 465 signature = typing.signature(state.return_type, *state.args) ~/miniconda3/envs/resistance-mechanisms/lib/python3.7/site-packages/numba/core/typed_passes.py in run_pass(self, state) 382 lower = lowering.Lower(targetctx, library, fndesc, interp, 383 metadata=metadata) --> 384 lower.lower() 385 if not flags.no_cpython_wrapper: 386 lower.create_cpython_wrapper(flags.release_gil) ~/miniconda3/envs/resistance-mechanisms/lib/python3.7/site-packages/numba/core/lowering.py in lower(self) 134 if self.generator_info is None: 135 self.genlower = None --> 136 self.lower_normal_function(self.fndesc) 137 else: 138 self.genlower = self.GeneratorLower(self) ~/miniconda3/envs/resistance-mechanisms/lib/python3.7/site-packages/numba/core/lowering.py in lower_normal_function(self, fndesc) 188 # Init argument values 189 self.extract_function_arguments() --> 190 entry_block_tail = self.lower_function_body() 191 192 # Close tail of entry block ~/miniconda3/envs/resistance-mechanisms/lib/python3.7/site-packages/numba/core/lowering.py in lower_function_body(self) 214 bb = self.blkmap[offset] 215 self.builder.position_at_end(bb) --> 216 self.lower_block(block) 217 self.post_lower() 218 return entry_block_tail ~/miniconda3/envs/resistance-mechanisms/lib/python3.7/site-packages/numba/core/lowering.py in lower_block(self, block) 228 with new_error_context('lowering "{inst}" at {loc}', inst=inst, 229 loc=self.loc, errcls_=defaulterrcls): --> 230 self.lower_inst(inst) 231 self.post_block(block) 232 ~/miniconda3/envs/resistance-mechanisms/lib/python3.7/contextlib.py in __exit__(self, type, value, traceback) 128 value = type() 129 try: --> 130 self.gen.throw(type, value, traceback) 131 except StopIteration as exc: 132 # Suppress StopIteration *unless* it's the same exception that ~/miniconda3/envs/resistance-mechanisms/lib/python3.7/site-packages/numba/core/errors.py in new_error_context(fmt_, *args, **kwargs) 749 newerr = errcls(e).add_context(_format_msg(fmt_, args, kwargs)) 750 tb = sys.exc_info()[2] if numba.core.config.FULL_TRACEBACKS else None --> 751 raise newerr.with_traceback(tb) 752 753 LoweringError: Failed in nopython mode pipeline (step: nopython mode backend) Storing i64 to ptr of i32 ('dim'). FE type int32 File "../../../../../../../miniconda3/envs/resistance-mechanisms/lib/python3.7/site-packages/umap/layouts.py", line 52: def rdist(x, y): <source elided> result = 0.0 dim = x.shape[0] ^ During: lowering "dim = static_getitem(value=$8load_attr.2, index=0, index_var=$const10.3, fn=<built-in function getitem>)" at /Users/gway/miniconda3/envs/resistance-mechanisms/lib/python3.7/site-packages/umap/layouts.py (52) LoweringError: Failed in nopython mode pipeline (step: nopython mode backend) Storing i64 to ptr of i32 ('dim'). FE type int32 File "../../../../../../../miniconda3/envs/resistance-mechanisms/lib/python3.7/site-packages/umap/layouts.py", line 52: def rdist(x, y): <source elided> result = 0.0 dim = x.shape[0] ^ During: lowering "dim = static_getitem(value=$8load_attr.2, index=0, index_var=$const10.3, fn=<built-in function getitem>)" at /Users/gway/miniconda3/envs/resistance-mechanisms/lib/python3.7/site-packages/umap/layouts.py (52)
In step 2, I ran into a new bug: