From c476ad45cb8b13fd86af39789c4aa16d220ffbdc Mon Sep 17 00:00:00 2001 From: phyng Date: Thu, 22 Jun 2023 22:21:42 +0800 Subject: [PATCH 1/5] feat(scilib): add more report support --- scilib/cnki/importer.py | 11 +++++++++-- scilib/cnki/report.py | 6 ++++-- scilib/wos/report.py | 6 +++++- 3 files changed, 18 insertions(+), 5 deletions(-) diff --git a/scilib/cnki/importer.py b/scilib/cnki/importer.py index 92db965..d0bb70b 100644 --- a/scilib/cnki/importer.py +++ b/scilib/cnki/importer.py @@ -161,9 +161,16 @@ def parse_txt_file(file_path): return articles.values() -def read_text_format_dir(from_dir): +def read_text_format_dir(from_dir, keyword_replace_map=None): for file in Path(from_dir).glob('**/*.txt'): - yield from parse_txt_file(file) + for item in parse_txt_file(file): + item['fu_tokens'] = parse_fu_tokens(item) + item['keyword_tokens'] = parse_keyword_tokens(item, keyword_replace_map=keyword_replace_map) + item['parsed_year'] = parse_year(item) + item['clc_tokens'] = parse_clc_tokens(item) + item['clc_level1_tokens'] = parse_clc_level1_tokens(item) + item['clc_level2_tokens'] = parse_clc_level2_tokens(item) + yield item def read_spider_format(file_path, *, fields=None, keyword_replace_map=None): diff --git a/scilib/cnki/report.py b/scilib/cnki/report.py index 743c187..a61b741 100644 --- a/scilib/cnki/report.py +++ b/scilib/cnki/report.py @@ -107,8 +107,9 @@ def report_cnki_keywords( cnki_items, *, outpur_dir, + top_size=50, ): - counter, corrs = get_corrs([item["keyword_tokens"] for item in cnki_items]) + counter, corrs = get_corrs([item["keyword_tokens"] for item in cnki_items], top_size=top_size) corrs_csv_string = corrs_to_csv_string(corrs) with open(os.path.join(outpur_dir, "keywords.corrs.csv"), "w") as f: f.write(corrs_csv_string) @@ -147,7 +148,8 @@ def report_cnki_all( cnki_items, *, outpur_dir, + keywords_top_size=50, ): pd.DataFrame.from_records(cnki_items).to_csv(os.path.join(outpur_dir, "items.csv"), index=False) - report_cnki_keywords(cnki_items, outpur_dir=outpur_dir) + report_cnki_keywords(cnki_items, outpur_dir=outpur_dir, top_size=keywords_top_size) report_cnki_org(cnki_items, outpur_dir=outpur_dir) diff --git a/scilib/wos/report.py b/scilib/wos/report.py index 8df8e84..9051993 100644 --- a/scilib/wos/report.py +++ b/scilib/wos/report.py @@ -48,6 +48,7 @@ def report_wos_keywords( outpur_dir, keyword_field="DE", keyword_replace_map=None, + top_size=50 ): keyword_tokens_list = [ parse_keyword_tokens(item, keyword_field=keyword_field, replace_map=keyword_replace_map) @@ -58,7 +59,7 @@ def report_wos_keywords( pd.DataFrame(counter_items).to_csv(os.path.join(outpur_dir, "keywords.counter.csv"), index=False) # corrs - _, corrs = get_corrs(keyword_tokens_list) + _, corrs = get_corrs(keyword_tokens_list, top_size=top_size) corrs_csv_string = corrs_to_csv_string(corrs) with open(os.path.join(outpur_dir, "keywords.corrs.csv"), "w") as f: f.write(corrs_csv_string) @@ -93,11 +94,14 @@ def report_wos_all( outpur_dir, keyword_field="DE", keyword_replace_map=None, + keywords_top_size=50, ): + pd.DataFrame.from_records(wos_items).to_csv(os.path.join(outpur_dir, "items.csv"), index=False) report_wos_keywords( wos_items, outpur_dir=outpur_dir, keyword_field=keyword_field, keyword_replace_map=keyword_replace_map, + top_size=keywords_top_size ) report_wos_org(wos_items, outpur_dir=outpur_dir) From 9b260e00c7a1486ce2dca4028a15f2ac08b20635 Mon Sep 17 00:00:00 2001 From: phyng Date: Sun, 14 Jan 2024 23:03:17 +0800 Subject: [PATCH 2/5] chore(project): update deps --- poetry.lock | 4857 +++++++++++++++--------------------------------- pyproject.toml | 6 +- 2 files changed, 1545 insertions(+), 3318 deletions(-) diff --git a/poetry.lock b/poetry.lock index 7897f09..d080ba5 100644 --- a/poetry.lock +++ b/poetry.lock @@ -1,10 +1,9 @@ -# This file is automatically @generated by Poetry and should not be changed by hand. +# This file is automatically @generated by Poetry 1.7.1 and should not be changed by hand. 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"pytest-mypy (>=0.9.1)"] +docs = ["furo", "jaraco.packaging (>=9.3)", "jaraco.tidelift (>=1.4)", "rst.linker (>=1.9)", "sphinx (<7.2.5)", "sphinx (>=3.5)", "sphinx-lint"] +testing = ["big-O", "jaraco.functools", "jaraco.itertools", "more-itertools", "pytest (>=6)", "pytest-black (>=0.3.7)", "pytest-checkdocs (>=2.4)", "pytest-cov", "pytest-enabler (>=2.2)", "pytest-ignore-flaky", "pytest-mypy (>=0.9.1)", "pytest-ruff"] [extras] -db = ["redis", "psycopg2", "SQLAlchemy", "pandas_access"] +db = ["SQLAlchemy", "pandas_access", "psycopg2", "redis"] gender = ["agefromname", "gender-guesser", "genderizer", "naiveBayesClassifier"] [metadata] lock-version = "2.0" python-versions = ">=3.9,<3.12" -content-hash = "c06ff0f53dc772b7bddd97434510ac80966e35eddcdb265ebc02b55c62bfd93e" +content-hash = "592ba6fdde9786d779bb62bc9da3d286dcf43c5f8ba4f99a0b26bfec2bfe6963" diff --git a/pyproject.toml b/pyproject.toml index 52f97a8..3b9ba40 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -21,7 +21,6 @@ scilib-gender-benchmark = "scilib.gender.benchmark.benchmark:run" [tool.poetry.dependencies] python = ">=3.9,<3.12" pandas = "^1.5.3" -jupyter = "^1.0.0" numpy = "^1.24.3" xlrd = "^2.0.1" matplotlib = "^3.7.1" @@ -34,7 +33,6 @@ pypinyin = "^0.48" tabulate = "^0.9.0" pyquery = "^2.0.0" libs = "^0.0.10" -jupyterlab = "^3.6.3" nameparser = "^1.1.2" Unidecode = "^1.3.6" aiohttp = "^3.8.4" @@ -64,5 +62,5 @@ db = ["redis", "psycopg2", "SQLAlchemy", "pandas_access"] gender = ["agefromname", "gender-guesser", "genderizer", "naiveBayesClassifier"] [build-system] -requires = ["poetry>=0.12"] -build-backend = "poetry.masonry.api" +requires = ["poetry-core"] +build-backend = "poetry.core.masonry.api" From bc150d94862b39acb9a3bb482bc40456a1a6b3bb Mon Sep 17 00:00:00 2001 From: phyng Date: Sun, 14 Jan 2024 23:03:57 +0800 Subject: [PATCH 3/5] perf(corr): add fast corr func --- scilib/corrs/corrs_utils.py | 61 ++++++++++++++++- scilib/tests/test_corrs.py | 130 ++++++++++++++++++++++++++++++++++++ 2 files changed, 190 insertions(+), 1 deletion(-) create mode 100644 scilib/tests/test_corrs.py diff --git a/scilib/corrs/corrs_utils.py b/scilib/corrs/corrs_utils.py index b17dbf1..4a8ca1a 100644 --- a/scilib/corrs/corrs_utils.py +++ b/scilib/corrs/corrs_utils.py @@ -2,9 +2,10 @@ from __future__ import unicode_literals, absolute_import, print_function, division from collections import Counter +import pandas as pd -def get_corrs(tokens_list, top_size=50): +def get_corrs_slow(tokens_list, top_size=50): counter = Counter([token for tokens in tokens_list for token in tokens]) top_n = [token for token, _ in counter.most_common(top_size)] @@ -18,6 +19,24 @@ def get_corrs(tokens_list, top_size=50): return [counter, corrs] +def get_corrs(tokens_list, top_size=50): + counter = Counter([token for tokens in tokens_list for token in tokens]) + top_n = [token for token, _ in counter.most_common(top_size)] + + # Initialize a dataframe to store the co-occurrence matrix + co_occurrence_matrix = pd.DataFrame(data=0, index=top_n, columns=top_n) + + for tokens in tokens_list: + # Only consider the tokens that are in top_n + tokens = set(tokens) & set(top_n) + for token1 in tokens: + for token2 in tokens: + co_occurrence_matrix.at[token1, token2] += 1 + + corrs = co_occurrence_matrix.reset_index().values.tolist() + return [counter, corrs] + + def corrs_to_csv_string(corrs, name_map=None): name_map = name_map or (lambda x: x) lines = [] @@ -26,6 +45,46 @@ def corrs_to_csv_string(corrs, name_map=None): return '\n'.join(lines) +def corrs_to_pnetview_json(corrs): + top_value = max([max(row[1:]) for row in corrs]) + names = [row[0] for row in corrs] + nodes = [] + edges = [] + for index, row in enumerate(corrs): + name = row[0] + count = row[index + 1] + node = { + "id": name, + "style": { + "keyshape": { + "size": 100 * count / top_value + }, + "label": { + "value": name + } + } + } + nodes.append(node) + for other_name in names[index + 1:]: + value = row[names.index(other_name) + 1] + edge = { + "source": name, + "target": other_name, + "value": value, + "style": { + "keyshape": { + "lineWidth": 20 * value / top_value + } + } + } + edges.append(edge) + + return { + "nodes": nodes, + "edges": edges + } + + def corrs_to_cortext_network(corrs, header=None, name_map=None): header = header or ['keyword1', 'keyword2'] name_map = name_map or (lambda x: x) diff --git a/scilib/tests/test_corrs.py b/scilib/tests/test_corrs.py new file mode 100644 index 0000000..ef8a825 --- /dev/null +++ b/scilib/tests/test_corrs.py @@ -0,0 +1,130 @@ +# coding: utf-8 + +from __future__ import unicode_literals, absolute_import, print_function, division + +from unittest import TestCase +from scilib.corrs.corrs_utils import get_corrs, get_corrs_slow, corrs_to_pnetview_json + + +class CorrsUtilsTest(TestCase): + + def test_get_corrs(self): + tokens_list = [ + ["a", "b", "c"], + ["a", "b", "d"], + ["a", "c", "d"], + ["b", "c", "d"], + ["b", "c", "e"], + ["c", "d", "e"], + ["c", "e", "f"], + ["d", "e", "f"], + ["e", "f", "g"], + ["f", "g", "h"], + ] + counter, corrs = get_corrs(tokens_list, top_size=3) + self.assertDictEqual(dict(counter.most_common(3)), {'c': 6, 'd': 5, 'e': 5}) + self.assertListEqual(corrs, [ + ['c', 6, 3, 3], + ['d', 3, 5, 2], + ['e', 3, 2, 5] + ]) + + def test_get_corrs_slow(self): + tokens_list = [ + ["a", "b", "c"], + ["a", "b", "d"], + ["a", "c", "d"], + ["b", "c", "d"], + ["b", "c", "e"], + ["c", "d", "e"], + ["c", "e", "f"], + ["d", "e", "f"], + ["e", "f", "g"], + ["f", "g", "h"], + ] + counter, corrs = get_corrs_slow(tokens_list, top_size=3) + self.assertDictEqual(dict(counter.most_common(3)), {'c': 6, 'd': 5, 'e': 5}) + self.assertListEqual(corrs, [ + ['c', 6, 3, 3], + ['d', 3, 5, 2], + ['e', 3, 2, 5] + ]) + + def test_corrs_to_pnetview_json(self): + corrs = [ + ['c', 6, 3, 3], + ['d', 3, 5, 2], + ['e', 3, 2, 5] + ] + expected_result = { + "nodes": [ + { + "id": "c", + "style": { + "keyshape": { + "size": 100 * 6 / 6 + }, + "label": { + "value": "c" + } + } + }, + { + "id": "d", + "style": { + "keyshape": { + "size": 100 * 5 / 6 + }, + "label": { + "value": "d" + } + } + }, + { + "id": "e", + "style": { + "keyshape": { + "size": 100 * 5 / 6 + }, + "label": { + "value": "e" + } + } + } + ], + "edges": [ + { + "source": "c", + "target": "d", + "value": 3, + "style": { + "keyshape": { + "lineWidth": 20 * 3 / 6 + } + } + }, + { + "source": "c", + "target": "e", + "value": 3, + "style": { + "keyshape": { + "lineWidth": 20 * 3 / 6 + } + } + }, + { + "source": "d", + "target": "e", + "value": 2, + "style": { + "keyshape": { + "lineWidth": 20 * 2 / 6 + } + } + } + ] + } + + self.assertListEqual(corrs_to_pnetview_json(corrs)['nodes'], expected_result['nodes']) + self.assertListEqual(corrs_to_pnetview_json(corrs)['edges'], expected_result['edges']) From b828ccd4baf78be8540181a8ff144f12ec72e948 Mon Sep 17 00:00:00 2001 From: phyng Date: Sun, 14 Jan 2024 23:04:30 +0800 Subject: [PATCH 4/5] feat(stata): update stata plugin --- scilib/antv/sankey.py | 3 ++- scilib/cnki/report.py | 21 +++++++++++++++++++-- scilib/stata/action.py | 15 ++++++++++++++- scilib/stata/plugin.py | 22 +++++++++++++++++++++ scilib/stata/run.py | 2 +- scilib/wos/importer.py | 5 ++++- scilib/wos/report.py | 43 ++++++++++++++++++++++++++++++++++++++++++ 7 files changed, 105 insertions(+), 6 deletions(-) diff --git a/scilib/antv/sankey.py b/scilib/antv/sankey.py index cca25fc..3bf8f47 100644 --- a/scilib/antv/sankey.py +++ b/scilib/antv/sankey.py @@ -3,6 +3,7 @@ from __future__ import unicode_literals, absolute_import, print_function, division import json +from typing import List import pandas as pd from optparse import OptionParser from collections import Counter @@ -35,7 +36,7 @@ def make_matrix_csv(nodes, edges): return '\n'.join(lines) -def make_sankey_data(nodes, edges): +def make_sankey_data(nodes: List[str], edges): data_nodes = [dict(name=node) for node in nodes] counter = Counter(edges) data_links = [] diff --git a/scilib/cnki/report.py b/scilib/cnki/report.py index a61b741..8c9dd2a 100644 --- a/scilib/cnki/report.py +++ b/scilib/cnki/report.py @@ -110,6 +110,8 @@ def report_cnki_keywords( top_size=50, ): counter, corrs = get_corrs([item["keyword_tokens"] for item in cnki_items], top_size=top_size) + top_n = [token for token, _ in counter.most_common(top_size)] + corrs_csv_string = corrs_to_csv_string(corrs) with open(os.path.join(outpur_dir, "keywords.corrs.csv"), "w") as f: f.write(corrs_csv_string) @@ -126,16 +128,27 @@ def report_cnki_keywords( with open(os.path.join(outpur_dir, "keywords.cortext.csv"), "w") as f: f.write(cortext_network_to_csv_string(cortext_network)) + # keywords_year_extend + top_keywords_year_extend = [] + # cortext network with year networks = {} for year in sorted(set([item["parsed_year"] for item in cnki_items if item["parsed_year"]])): year_items = [item for item in cnki_items if item["parsed_year"] == year] - _, year_corrs = get_corrs([item["keyword_tokens"] for item in year_items]) + year_counter, year_corrs = get_corrs([item["keyword_tokens"] for item in year_items]) networks[int(year)] = corrs_to_cortext_network(year_corrs) + for k, v in year_counter.most_common(): + if k in top_n: + top_keywords_year_extend.extend(dict(year=year, keyword=k) for i in range(v)) + year_cortext_networks = merge_year_cortext_networks(networks) with open(os.path.join(outpur_dir, "keywords.cortext_with_year.csv"), "w") as f: f.write(cortext_network_to_csv_string(year_cortext_networks)) + pd.DataFrame.from_records(top_keywords_year_extend).to_csv( + os.path.join(outpur_dir, "keywords.top.year_extend.csv"), index=False + ) + # pnetview txt format pnetview_text = '\n'.join( [','.join(uniqify([t.replace(',', '-') for t in item["keyword_tokens"]])) for item in cnki_items] @@ -151,5 +164,9 @@ def report_cnki_all( keywords_top_size=50, ): pd.DataFrame.from_records(cnki_items).to_csv(os.path.join(outpur_dir, "items.csv"), index=False) - report_cnki_keywords(cnki_items, outpur_dir=outpur_dir, top_size=keywords_top_size) + report_cnki_keywords( + cnki_items, + outpur_dir=outpur_dir, + top_size=keywords_top_size + ) report_cnki_org(cnki_items, outpur_dir=outpur_dir) diff --git a/scilib/stata/action.py b/scilib/stata/action.py index 1935ba9..d33a9df 100644 --- a/scilib/stata/action.py +++ b/scilib/stata/action.py @@ -3,7 +3,7 @@ from __future__ import unicode_literals, absolute_import, print_function, division from itertools import combinations -from .plugin import summary, reg, nbreg, psm, margins, label +from .plugin import summary, reg, nbreg, psm, margins, label, teteffects, did def use_actions(actions, config_actions): @@ -21,6 +21,19 @@ def use_actions(actions, config_actions): actions.append(margins(action["vars"], title=action.get('title'), xtitle=action.get('xtitle'), ytitle=action.get('ytitle'))) # noqa elif action['type'] == 'psm': actions.append(psm(action["treatVar"], action["vars"], action["depVar"])) + elif action['type'] == 'teteffects': + actions.append(teteffects(action["treatVar"], action["vars"], action["depVar"])) + elif action['type'] == 'did': + """ + { + "type": "did", + "time": "time", + "treated": "treated", + "y": "y", + "cov": "x1 x2 x3" + } + """ + actions.append(did(action["time"], action["treated"], action["y"], action["cov"])) elif action['type'] == 'combinations': for var_list in combinations(action['vars'].split(), action['count']): for _action in action['actions']: diff --git a/scilib/stata/plugin.py b/scilib/stata/plugin.py index a102bb6..455511c 100644 --- a/scilib/stata/plugin.py +++ b/scilib/stata/plugin.py @@ -85,6 +85,28 @@ def margins(var_list, title=None, xtitle=None, ytitle=None): ) +def teteffects(var_treat, var_deps, var_result): + return call_batch( + call('* teteffects ipw'), + call(f'teffects ipw ({var_result}) ({var_treat} {var_deps})'), + + call('* teteffects aipw'), + call(f'teffects aipw ({var_result}) ({var_treat} {var_deps})'), + ) + + +def did(time, treated, y, cov=''): + return call_batch( + call('* DID 分析'), + call(f'reg {y} {time}##{treated} {cov}, r'), + call(f'diff {y}, t({treated}) p({time}) {f"cov({cov})" if cov else ""}'), + call(f'diff {y}, t({treated}) p({time}) {f"cov({cov})" if cov else ""} test'), + call(f'collapse (mean) {y}, by({time} {treated})'), + call(f'twoway (line {y} {time} if {treated}==1) (line {y} {time} if {treated}==0), legend(label(1 Treated) label(2 Control))'), # noqa + call('graph export did.pdf, replace'), + ) + + def psm(var_treat, var_deps, var_result, word_file='mytable.docx'): def graph(suffix): diff --git a/scilib/stata/run.py b/scilib/stata/run.py index 384f3ea..33e1501 100644 --- a/scilib/stata/run.py +++ b/scilib/stata/run.py @@ -25,7 +25,7 @@ filemode='a', ) -STATA_ENTRY = os.environ.get('STATA_ENTRY', '/Applications/Stata/StataSE.app/Contents/MacOS/StataSE') +STATA_ENTRY = os.environ.get('STATA_ENTRY', '/Applications/Stata/StataMP.app/Contents/MacOS/StataMP') logger = logging.getLogger('stata') logger.addHandler(logging.StreamHandler()) diff --git a/scilib/wos/importer.py b/scilib/wos/importer.py index abaa42e..9ea0608 100644 --- a/scilib/wos/importer.py +++ b/scilib/wos/importer.py @@ -73,9 +73,12 @@ def read_text_format_path(path, *, export_type='other_text'): def scan_text_format_dir(abs_path, *, globs=None): globs = globs or ['**/*.txt', '**/*.csv', '*.csv', '*.txt'] + paths = set() for glob in globs: for path in Path(abs_path).glob(glob): - yield path + if str(path) not in paths: + paths.add(str(path)) + yield path def read_text_format_dir(abs_path, *, globs=None, export_type='other_text'): diff --git a/scilib/wos/report.py b/scilib/wos/report.py index 9051993..5708b0a 100644 --- a/scilib/wos/report.py +++ b/scilib/wos/report.py @@ -2,10 +2,12 @@ from __future__ import unicode_literals, absolute_import, print_function, division from collections import Counter +import json import os import pandas as pd from scilib.corrs.corrs_utils import ( + corrs_to_pnetview_json, get_corrs, corrs_to_csv_string, corrs_to_cortext_network, @@ -88,6 +90,43 @@ def report_wos_keywords( f.write(pnetview_text) +def report_country(wos_items, *, outpur_dir, country_map): + prefix = 'country.with_country_map' if country_map else 'country' + for field in ['countrys_c1_rp', 'countrys_rp', 'first_country']: + countrys_list = [] + year_countrys_list = {} + total_count = 0 + for item in wos_items: + if field == 'first_country': + countrys = [item['first_country']] if item['first_country'] else [] + else: + countrys = list(set(item[field])) + + # map and filter by country_map + if country_map: + countrys = [country_map.get(i, i) for i in countrys] + countrys = [i for i in countrys if i] + if not countrys: + continue + + total_count += 1 + countrys_list.append(countrys) + if item.get('PY'): + year_countrys_list.setdefault(item['PY'], []).append(countrys) + + with open(os.path.join(outpur_dir, f'{prefix}.{field}.count.csv'), 'w') as f: + f.write(str(total_count)) + + for size in [50, 100]: + _, corrs = get_corrs(countrys_list, top_size=size) + csv = corrs_to_csv_string(corrs) + with open(os.path.join(outpur_dir, f'{prefix}.{field}.corr.{size}.csv'), 'w') as f: + f.write(csv) + pnetview_json = corrs_to_pnetview_json(corrs) + with open(os.path.join(outpur_dir, f'{prefix}.{field}.pnetview.{size}.json'), 'w') as f: + json.dump(pnetview_json, f) + + def report_wos_all( wos_items, *, @@ -95,6 +134,7 @@ def report_wos_all( keyword_field="DE", keyword_replace_map=None, keywords_top_size=50, + country_map=None ): pd.DataFrame.from_records(wos_items).to_csv(os.path.join(outpur_dir, "items.csv"), index=False) report_wos_keywords( @@ -105,3 +145,6 @@ def report_wos_all( top_size=keywords_top_size ) report_wos_org(wos_items, outpur_dir=outpur_dir) + report_country(wos_items, outpur_dir=outpur_dir, country_map=None) + if country_map: + report_country(wos_items, outpur_dir=outpur_dir, country_map=country_map) From a701618dbb4f912ef5c6b381fad44b93ad244dcb Mon Sep 17 00:00:00 2001 From: phyng Date: Sun, 14 Jan 2024 23:11:15 +0800 Subject: [PATCH 5/5] chore(ci): update githubpages workflow --- .github/workflows/githubpages.yaml | 6 ++---- 1 file changed, 2 insertions(+), 4 deletions(-) diff --git a/.github/workflows/githubpages.yaml b/.github/workflows/githubpages.yaml index b34f24a..aedcc03 100644 --- a/.github/workflows/githubpages.yaml +++ b/.github/workflows/githubpages.yaml @@ -30,8 +30,6 @@ jobs: touch build/html/.nojekyll - name: Deploy - uses: JamesIves/github-pages-deploy-action@releases/v3 + uses: JamesIves/github-pages-deploy-action@releases/v4 with: - ACCESS_TOKEN: ${{ secrets.ACCESS_TOKEN }} - BRANCH: gh-pages # The branch the action should deploy to. - FOLDER: build/html # The folder the action should deploy. + folder: build/html # The folder the action should deploy.