FileNotFoundError: [Errno 2] No such file or directory: '/home/biomamba/miniconda3/envs/stereopy/lib/python3.8/site-packages/stereopy-0.14.0b1-py3.8.egg/stereo/algorithm/ccd/assets/favicon.ico'

STOmics / Stereopy

A toolkit of spatial transcriptomic analysis.

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Cell communities clustering report

Parameters used
Annotation	{params['annotation']}
Resolution	{params['resolution']}
Spot size	{params['spot_size']}
Total cells normalization	{params['total_cell_norm']}
Downsample rate	{params['downsample_rate']}
Entropy threshold	{params['entropy_thres']}
Scatteredness threshold	{params['scatter_thres']}
Window sizes	{params['win_sizes']}
Sliding steps	{params['sliding_steps']}

Parameters used

Annotation

{params['annotation']}

Resolution

{params['resolution']}

Spot size

{params['spot_size']}

Total cells normalization

{params['total_cell_norm']}

Downsample rate

{params['downsample_rate']}

Entropy threshold

{params['entropy_thres']}

Scatteredness threshold

{params['scatter_thres']}

Window sizes

{params['win_sizes']}

Sliding steps

{params['sliding_steps']}

Per community

File ~/miniconda3/envs/stereopy/lib/python3.8/site-packages/stereopy-0.14.0b1-py3.8.egg/stereo/algorithm/ccd/html_report.py:22, in get_base64_encoded_img(path) 12 def get_base64_encoded_img(path): 13 """ 14 Get the base64-encoded representation of an image. 15 (...) 20 - str: A base64-encoded string representing the image. 21 """ ---> 22 data_uri = base64.b64encode(open(path, 'rb').read()).decode('utf-8') 23 return '"data:image/png;base64,{0}"'.format(data_uri)

FileNotFoundError: [Errno 2] No such file or directory: '/home/biomamba/miniconda3/envs/stereopy/lib/python3.8/site-packages/stereopy-0.14.0b1-py3.8.egg/stereo/algorithm/ccd/assets/favicon.ico'`

It seems to cause many bugs after I update the stereopy into version 0.04.0b1. Meanwhile, many fonctions also can't work in older version. It realy confused me. Cloud you please tell me how to solve it?

Biomamba commented 11 months ago

Dear author: I have met a new problem when I study the CCD workflow in stereopy-0.14.0b1. `ccd = data.tl.community_detection( annotation='sim anno', out_path='results/whole_brain', win_sizes='150', sliding_steps='50', scatter_thres=0.12, downsample_rate=80, cluster_algo='agglomerative', n_clusters=16, resolution=0.25, plotting=5, hide_plots=True ) File ~/miniconda3/envs/stereopy/lib/python3.8/site-packages/stereopy-0.14.0b1-py3.8.egg/stereo/algorithm/community_detection.py:769, in CommunityDetection.main(self, kwargs) 692 r""" 693 694 CCD divides the tissue using sliding windows by accommodating multiple window sizes, and enables the simultaneous analysis of multiple slices from the same tissue. CCD consists of the three main steps: (...) 764 :return: Object of CommunityDetection. 765 """ 767 assert type(self.stereo_exp_data) is AnnBasedStereoExpData, 768 "this method can only run with AnnBasedStereoExpData temporarily" --> 769 self._main([self.stereo_exp_data], kwargs) 770 return self

File ~/miniconda3/envs/stereopy/lib/python3.8/site-packages/stereopy-0.14.0b1-py3.8.egg/stereo/algorithm/ccd/utils.py:24, in timeit..timeit_wrapper(*args, kwargs) 21 @wraps(func) 22 def timeit_wrapper(*args, *kwargs): 23 start_time = time.perf_counter() ---> 24 result = func(args, kwargs) 25 end_time = time.perf_counter() 26 total_time = end_time - start_time

File ~/miniconda3/envs/stereopy/lib/python3.8/site-packages/stereopy-0.14.0b1-py3.8.egg/stereo/algorithm/community_detection.py:263, in _CommunityDetection._main(self, slices, annotation, **kwargs) 260 end_time = time.perf_counter() 262 self.params['execution_time'] = end_time - start_time --> 263 generate_report(self.params)

File ~/miniconda3/envs/stereopy/lib/python3.8/site-packages/stereopy-0.14.0b1-py3.8.egg/stereo/algorithm/ccd/utils.py:24, in timeit..timeit_wrapper(*args, kwargs) 21 @wraps(func) 22 def timeit_wrapper(*args, *kwargs): 23 start_time = time.perf_counter() ---> 24 result = func(args, kwargs) 25 end_time = time.perf_counter() 26 total_time = end_time - start_time

File ~/miniconda3/envs/stereopy/lib/python3.8/site-packages/stereopy-0.14.0b1-py3.8.egg/stereo/algorithm/ccd/html_report.py:413, in generate_report(params) 369 created_time = f"Report created at {commit_date}" 371 annotation_figure, communities_figure = annotation_and_communities_figures(params['out_path']) 373 htmlstr = f''' 374 375 376 377 378 381 382 411 412 Cell Communities Report --> 413 <link rel="icon" type="image/png" sizes="16x16" href={get_base64_encoded_img(f"{os.path.dirname(file)}/assets/favicon.ico")}/> 414 415 416 417

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Cell communities clustering report

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Parameters used

Annotation {params['annotation']} Resolution {params['resolution']} Spot size {params['spot_size']} Total cells normalization {params['total_cell_norm']} Downsample rate {params['downsample_rate']} Entropy threshold {params['entropy_thres']} Scatteredness threshold {params['scatter_thres']} Window sizes {params['win_sizes']} Sliding steps {params['sliding_steps']}

470 Copy command

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Overall

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Cell type annotation:

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Communities obtained:

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491 492 493 494

495 <div class="centered testRemove" data-value={"remove" if params['plotting'] < 3 else "keep"}> 496

Cell mixtures for all slices:

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498 <div class="centered testRemove" data-value={"remove" if params['plotting'] < 3 else "keep"}> 499 500 <img title="Showing the percentage of each cell type within obtained community and corresponding sums" src={all_slices_get_figure(params['out_path'], "total_cell_mixtures_table.png", params['plotting'])}> 501 502

503 <div class="centered testRemove" data-value={"remove" if params['plotting'] < 3 else "keep"}> 504

Cell type abundance:

505 506 <div class="centered testRemove" data-value={"remove" if params['plotting'] < 3 else "keep"}> 507 508 <img title="Percentage of specific cell types per slice" src={all_slices_get_figure(params['out_path'], "cell_abundance_all_slices.png", params['plotting'])}> 509 510 511 <div class="centered testRemove" data-value={"remove" if params['plotting'] < 3 else "keep"}> 512

Communities abundance:

513 514 <div class="centered testRemove" data-value={"remove" if params['plotting'] < 3 else "keep"}> 515 516 <img title="Percentage of cells in each community per slice" src={all_slices_get_figure(params['out_path'], "cluster_abundance_all_slices.png", params['plotting'])}> 517 518 519 <div class="centered testRemove" data-value={"remove" if params['plotting'] < 4 else "keep"}> 520

Cell percentage in communities:

521 </div class="centered testRemove"> 522 <div class="centered testRemove" data-value={"remove" if params['plotting'] < 4 else "keep"}> 523 524 <img title="Percentage of cells in each community per slice" src={all_slices_get_figure(params['out_path'], "cell_perc_in_community_per_slice.png", params['plotting'])}> 525 526 527

528 <div data-value={"remove" if params['plotting'] < 2 else "keep"}> 529

Per slice

530 531 <div class="testRemove" data-value={"remove" if params['plotting'] < 2 else "keep"}> 532 {per_slice_content(params['out_path'], params['plotting'])} 533 534

535 <div class="testRemove" data-value={"remove" if params['plotting'] < 3 else "keep"}> 536

Per community

537 538 <div class="centeredSmall" data-value={"remove" if params['plotting'] < 3 else "keep"}> 539 {per_community_content(params['out_path'], params['plotting'])} 540 541 542

{created_time}

543 544 545 546 ''' 548 with open(f"{params['out_path']}/report.html", "w") as f: 549 f.write(htmlstr) File ~/miniconda3/envs/stereopy/lib/python3.8/site-packages/stereopy-0.14.0b1-py3.8.egg/stereo/algorithm/ccd/html_report.py:22, in get_base64_encoded_img(path) 12 def get_base64_encoded_img(path): 13 """ 14 Get the base64-encoded representation of an image. 15 (...) 20 - str: A base64-encoded string representing the image. 21 """ ---> 22 data_uri = base64.b64encode(open(path, 'rb').read()).decode('utf-8') 23 return '"data:image/png;base64,{0}"'.format(data_uri)

FileNotFoundError: [Errno 2] No such file or directory: '/home/biomamba/miniconda3/envs/stereopy/lib/python3.8/site-packages/stereopy-0.14.0b1-py3.8.egg/stereo/algorithm/ccd/assets/favicon.ico'`

It seems to cause many bugs after I update the stereopy into version 0.04.0b1. Meanwhile, many fonctions also can't work in older version. It realy confused me. Cloud you please tell me how to solve it?

I have solved this problem by copying favicon.ico file to the corresponding directory.

STOmics / Stereopy