Merge branch 'NickSwainston:main' into main

NickSwainston · Jan 17, 2024 · 72ab5eb · 72ab5eb
2 parents d2ae15b + 8742668
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diff --git a/.github/workflows/update_cat_csv.yaml b/.github/workflows/update_cat_csv.yaml
@@ -0,0 +1,42 @@
+name: Update CSV and Commit
+
+env:
+  BRANCH_NAME: ${{ github.head_ref || github.ref_name }}
+
+on:
+  push:
+    branches:
+      - main
+    paths:
+      - pulsar_spectra/catalogue.py
+  pull_request:
+    paths:
+      - pulsar_spectra/catalogue.py
+
+jobs:
+  update-csv:
+    runs-on: ubuntu-latest
+
+    steps:
+      - name: Checkout Repository
+        uses: actions/checkout@v2
+
+      - name: Set up Python
+        uses: actions/setup-python@v2
+        with:
+          python-version: 3.8
+
+      - name: Install python dependencies
+        run: |
+          pip install .
+
+      - name: Run Update Script
+        run: |
+          cd docs
+          python get_ref_number_freq_range.py
+
+      - name: Commit Changes
+        uses: stefanzweifel/git-auto-commit-action@v5
+        with:
+          file_pattern: 'docs/papers_in_catalogue.csv'
+          commit_message: 'Update papers_in_catalogue.csv file [skip ci]'
diff --git a/docs/catalogue.rst b/docs/catalogue.rst
@@ -80,77 +80,7 @@ Papers included in our catalogue
 
 .. csv-table:: Papers included in our catalogue
     :header: "Paper","# Pulsars","Frequency range (MHz)","Link"
-
-    "ATNF pulsar catalogue","2863","40-150000","`Catalogue website <https://www.atnf.csiro.au/research/pulsar/psrcat/>`_"
-    "Bartel et al. (1978)","18","14800-22700","`ADS <https://ui.adsabs.harvard.edu/abs/1978A%26A....68..361B/abstract>`_"
-    "Manchester et al. (1978a)","224","40-408","`ADS <https://ui.adsabs.harvard.edu/abs/1978MNRAS.185..409M/abstract>`_"
-    "Izvekova et al. (1981)","86","39-102","`ADS <https://ui.adsabs.harvard.edu/abs/1981Ap%26SS..78...45I/abstract>`_"
-    "Dewey et al. (1985)","34","390-390","`ADS <https://ui.adsabs.harvard.edu/abs/1985ApJ...294L..25D/abstract>`_"
-    "McConnell et al. (1991)","4","610-610","`ADS <https://ui.adsabs.harvard.edu/abs/1991MNRAS.249..654M/abstract>`_"
-    "Johnston et al. (1992)","100","640-1577","`ADS <https://ui.adsabs.harvard.edu/abs/1992MNRAS.255..401J/abstract>`_"
-    "Wolszczan et al. (1992)","1","430-1400","`ADS <https://ui.adsabs.harvard.edu/abs/1992Natur.355..145W/abstract>`_"
-    "Johnston et al. (1993)","1","430-2360","`ADS <https://ui.adsabs.harvard.edu/abs/1993Natur.361..613J/abstract>`_"
-    "Manchester et al. (1993)","1","660-660","`ADS <https://ui.adsabs.harvard.edu/abs/1993ApJ...403L..29M/abstract>`_"
-    "Camilo et al. (1995)","29","430-430","`ADS <https://ui.adsabs.harvard.edu/abs/1995ApJ...445..756C/abstract>`_"
-    "Lundgren et al. (1995)","1","430-1400","`ADS <https://ui.adsabs.harvard.edu/abs/1995ApJ...453..419L/abstract>`_"
-    "Nicastro et al. (1995)","1","411-1400","`ADS <https://ui.adsabs.harvard.edu/abs/1995MNRAS.273L..68N/abstract>`_"
-    "Qiao et al. (1995)","61","660-1440","`ADS <https://ui.adsabs.harvard.edu/abs/1995MNRAS.274..572Q/abstract>`_"
-    "Robinson et al. (1995)","2","436-640","`ADS <https://ui.adsabs.harvard.edu/abs/1995MNRAS.274..547R/abstract>`_"
-    "Lorimer et al. (1995b)","280","408-1606","`ADS <https://ui.adsabs.harvard.edu/abs/1995MNRAS.273..411L/abstract>`_"
-    "Manchester et al. (1996)","55","436-436","`ADS <https://ui.adsabs.harvard.edu/abs/1996MNRAS.279.1235M/abstract>`_"
-    "Zepka et al. (1996)","1","430-1400","`ADS <https://ui.adsabs.harvard.edu/abs/1996ApJ...456..305Z/abstract>`_"
-    "van Ommen et al. (1997)","82","800-960","`ADS <https://ui.adsabs.harvard.edu/abs/1997MNRAS.287..307V/abstract>`_"
-    "Kramer et al. (1998)","34","1400-1400","`ADS <https://ui.adsabs.harvard.edu/abs/1998ApJ...501..270K/abstract>`_"
-    "Toscano et al. (1998)","19","436-1660","`ADS <https://ui.adsabs.harvard.edu/abs/1998ApJ...506..863T/abstract>`_"
-    "Kramer et al. (1999)","15","2695-4850","`ADS <https://ui.adsabs.harvard.edu/abs/1999ApJ...526..957K/abstract>`_"
-    "Stairs et al. (1999)","19","410-1414","`ADS <https://ui.adsabs.harvard.edu/abs/1999ApJS..123..627S/abstract>`_"
-    "Lommen et al. (2000)","3","430-1400","`ADS <https://ui.adsabs.harvard.edu/abs/2000ApJ...545.1007L/abstract>`_"
-    "Malofeev et al. (2000)","212","102-102","`ADS <https://ui.adsabs.harvard.edu/abs/2000ARep...44..436M/abstract>`_"
-    "Kuzmin et al. (2001)","30","102-111","`ADS <https://ui.adsabs.harvard.edu/abs/2001A%26A...368..230K/abstract>`_"
-    "Manchester et al. (2001)","100","1374-1374","`ADS <https://ui.adsabs.harvard.edu/abs/2001MNRAS.328...17M/abstract>`_"
-    "Morris et al. (2002)","120","1374-1374","`ADS <https://ui.adsabs.harvard.edu/abs/2002MNRAS.335..275M/abstract>`_"
-    "Kramer et al. (2003a)","200","1374-1374","`ADS <https://ui.adsabs.harvard.edu/abs/2003MNRAS.342.1299K/abstract>`_"
-    "Hobbs et al. (2004a)","453","1400-1400","`ADS <https://ui.adsabs.harvard.edu/abs/2004MNRAS.352.1439H/abstract>`_"
-    "Karastergiou et al. (2005)","48","3100-3100","`ADS <https://ui.adsabs.harvard.edu/abs/2005MNRAS.359..481K/abstract>`_"
-    "Johnston et al. (2006)","31","8356-8356","`ADS <https://ui.adsabs.harvard.edu/abs/2006MNRAS.369.1916J/abstract>`_"
-    "Lorimer et al. (2006)","142","1374-1374","`ADS <https://ui.adsabs.harvard.edu/abs/2006MNRAS.372..777L/abstract>`_"
-    "Kijak et al. (2007)","11","325-1060","`ADS <https://ui.adsabs.harvard.edu/abs/2007A%26A...462..699K/abstract>`_"
-    "Stappers et al. (2008)","13","147-147","`ADS <https://ui.adsabs.harvard.edu/abs/2008AIPC..983..593S/abstract>`_"
-    "Bates et al. (2011)","18","6591-6591","`ADS <https://ui.adsabs.harvard.edu/abs/2011MNRAS.411.1575B/abstract>`_"
-    "Keith et al. (2011)","9","17000-24000","`ADS <https://ui.adsabs.harvard.edu/abs/2011MNRAS.416..346K/abstract>`_"
-    "Kijak et al. (2011)","15","610-4850","`ADS <https://ui.adsabs.harvard.edu/abs/2011A%26A...531A..16K/abstract>`_"
-    "Zakharenko et al. (2013)","40","20-25","`ADS <https://ui.adsabs.harvard.edu/abs/2013MNRAS.431.3624Z/abstract>`_"
-    "Dembska et al. (2014)","19","610-8350","`ADS <https://ui.adsabs.harvard.edu/abs/2014MNRAS.445.3105D/abstract>`_"
-    "Dai et al. (2015)","24","730-3100","`ADS <https://ui.adsabs.harvard.edu/abs/2015MNRAS.449.3223D/abstract>`_"
-    "Stovall et al. (2015)","36","35-79","`ADS <https://ui.adsabs.harvard.edu/abs/2015ApJ...808..156S/abstract>`_"
-    "Basu et al. (2016)","1","325-1280","`ADS <https://ui.adsabs.harvard.edu/abs/2016MNRAS.458.2509B/abstract>`_"
-    "Bell et al. (2016)","17","154-154","`ADS <https://ui.adsabs.harvard.edu/abs/2016MNRAS.461..908B/abstract>`_"
-    "Bilous et al. (2016)","158","149-149","`ADS <https://ui.adsabs.harvard.edu/abs/2016A%26A...591A.134B/abstract>`_"
-    "Frail et al. (2016)","200","147-147","`ADS <https://ui.adsabs.harvard.edu/abs/2016ApJ...829..119F/abstract>`_"
-    "Han et al. (2016)","204","1274-1523","`ADS <https://ui.adsabs.harvard.edu/abs/2016RAA....16..159H/abstract>`_"
-    "Kondratiev et al. (2016)","48","149-149","`ADS <https://ui.adsabs.harvard.edu/abs/2016A%26A...585A.128K/abstract>`_"
-    "Kijak et al. (2017)","12","325-610","`ADS <https://ui.adsabs.harvard.edu/abs/2017ApJ...840..108K/abstract>`_"
-    "Mignani et al. (2017)","1","97500-343500","`ADS <https://ui.adsabs.harvard.edu/abs/2017ApJ...851L..10M/abstract>`_"
-    "Murphy et al. (2017)","60","76-227","`ADS <https://ui.adsabs.harvard.edu/abs/2017PASA...34...20M/abstract>`_"
-    "Xue et al. (2017)","48","185-185","`ADS <https://ui.adsabs.harvard.edu/abs/2017PASA...34...70X/abstract>`_"
-    "Jankowski et al. (2018)","441","728-3100","`ADS <https://ui.adsabs.harvard.edu/abs/2018MNRAS.473.4436J/abstract>`_"
-    "Johnston et al. (2018)","586","1360-1360","`ADS <https://ui.adsabs.harvard.edu/abs/2018MNRAS.474.4629J/abstract>`_"
-    "Jankowski et al. (2019)","205","843-843","`ADS <https://ui.adsabs.harvard.edu/abs/2019MNRAS.484.3691J/abstract>`_"
-    "Kaur et al. (2019)","1","81-3100","`ADS <https://ui.adsabs.harvard.edu/abs/2019ApJ...882..133K/abstract>`_"
-    "Sanidas et al. (2019)","288","135-135","`ADS <https://ui.adsabs.harvard.edu/abs/2019A%26A...626A.104S/abstract>`_"
-    "Xie et al. (2019)","32","1369-1369","`ADS <https://ui.adsabs.harvard.edu/abs/2019RAA....19..103X/abstract>`_"
-    "Zhang et al. (2019)","3","768-3968","`ADS <https://ui.adsabs.harvard.edu/abs/2019ApJ...885L..37Z/abstract>`_"
-    "Zhao et al. (2019)","71","4820-5124","`ADS <https://ui.adsabs.harvard.edu/abs/2019ApJ...874...64Z/abstract>`_"
-    "Bilous et al. (2020)","43","53-63","`ADS <https://ui.adsabs.harvard.edu/abs/2020A%26A...635A..75B/abstract>`_"
-    "Bondonneau et al. (2020)","64","53-65","`ADS <https://ui.adsabs.harvard.edu/abs/2020A%26A...635A..76B/abstract>`_"
-    "McEwen et al. (2020)","670","350-350","`ADS <https://ui.adsabs.harvard.edu/abs/2020ApJ...892...76M/abstract>`_"
-    "Alam et al. (2021)","47","430-2100","`ADS <https://ui.adsabs.harvard.edu/abs/2021ApJS..252....4A/abstract>`_"
-    "Bondonneau et al. (2021)","12","50-50","`ADS <https://ui.adsabs.harvard.edu/abs/2021A%26A...652A..34B/abstract>`_"
-    "Han et al. (2021)","201","1250-1250","`ADS <https://ui.adsabs.harvard.edu/abs/2021RAA....21..107H/abstract>`_"
-    "Johnston et al. (2021)","44","1369-1369","`ADS <https://ui.adsabs.harvard.edu/abs/2021MNRAS.502.1253J/abstract>`_"
-    "Kravtsov et al. (2022)","20","24-24","`ADS <https://ui.adsabs.harvard.edu/abs/2022MNRAS.512.4324K/abstract>`_"
-    "Lee et al. (2022)","22","70-352","`ADS <https://ui.adsabs.harvard.edu/abs/2022PASA...39...42L/abstract>`_"
-    "Spiewak et al. (2022)","189","1284-1284","`ADS <https://ui.adsabs.harvard.edu/abs/2022PASA...39...27S/abstract>`_"
+    :file: papers_in_catalogue.csv
 
 
 .. _finding_papers:

diff --git a/docs/get_ref_number_freq_range.py b/docs/get_ref_number_freq_range.py
@@ -38,41 +38,43 @@
             if jname not in pulsar_track:
                 pulsar_count += 1
                 pulsar_track.append(jname)
-if paper_format:
-    print(f"ATNF pulsar catalogue & {pulsar_count} & {int(min(all_freq))}-{int(max(all_freq))} \\\\")
-else:
-    print(f'"ATNF pulsar catalogue","{pulsar_count}","{int(min(all_freq))}-{int(max(all_freq))}","`Catalogue website <https://www.atnf.csiro.au/research/pulsar/psrcat/>`_"')
 
 
-# Loop over catalogues and put them into a dictionary
-for cat_file in CAT_YAMLS:
-    cat_label = cat_file.split("/")[-1].split(".")[0]
+with open("papers_in_catalogue.csv", "w") as output:
+    if paper_format:
+        output.write(f"ATNF pulsar catalogue & {pulsar_count} & {int(min(all_freq))}-{int(max(all_freq))} \\\\\n")
+    else:
+        output.write(f'"ATNF pulsar catalogue","{pulsar_count}","{int(min(all_freq))}-{int(max(all_freq))}","`Catalogue website <https://www.atnf.csiro.au/research/pulsar/psrcat/>`_"\n')
 
-    # Load in the dict
-    with open(cat_file, "r") as stream:
-        cat_dict = yaml.safe_load(stream)
-    pulsar_count = len(cat_dict.keys())
+    # Loop over catalogues and put them into a dictionary
+    for cat_file in CAT_YAMLS:
+        cat_label = cat_file.split("/")[-1].split(".")[0]
 
-    all_freq = []
-    # Find which pulsars in the dictionary
-    for jname in jnames:
-        if jname in cat_dict.keys():
-            # Update dict
-            jname_cat_dict[jname][cat_label] = cat_dict[jname]
-            # add freq
-            all_freq += cat_dict[jname]['Frequency MHz']
+        # Load in the dict
+        with open(cat_file, "r") as stream:
+            cat_dict = yaml.safe_load(stream)
+        pulsar_count = len(cat_dict.keys())
 
-    # output result
-    if paper_format:
-        cat_label = cat_label.replace("_", "")
-        print(f"\cite{{{cat_label}}} & {pulsar_count} & {int(min(all_freq))}-{int(max(all_freq))} \\\\")
-    else:
-        ads_link = ADS_REF[cat_label]
-        if cat_label == "Sieber_1973":
-            cat_label = "Sieber (1973)"
+        all_freq = []
+        # Find which pulsars in the dictionary
+        for jname in jnames:
+            if jname in cat_dict.keys():
+                # Update dict
+                jname_cat_dict[jname][cat_label] = cat_dict[jname]
+                # add freq
+                all_freq += cat_dict[jname]['Frequency MHz']
+
+        # output result
+        if paper_format:
+            cat_label = cat_label.replace("_", "")
+            output.write(f"\cite{{{cat_label}}} & {pulsar_count} & {int(min(all_freq))}-{int(max(all_freq))} \\\\\n")
         else:
-            author = " ".join(cat_label.split("_")[:-1])
-            year = cat_label.split("_")[-1]
-            cat_label = f"{author} et al. ({year})"
-        print(f'"{cat_label}","{pulsar_count}","{int(min(all_freq))}-{int(max(all_freq))}","`ADS <{ads_link}>`_"')
-    #print(all_freq)
+            ads_link = ADS_REF[cat_label]
+            if cat_label == "Sieber_1973":
+                cat_label = "Sieber (1973)"
+            else:
+                author = " ".join(cat_label.split("_")[:-1])
+                year = cat_label.split("_")[-1]
+                cat_label = f"{author} et al. ({year})"
+            output.write(f'"{cat_label}","{pulsar_count}","{int(min(all_freq))}-{int(max(all_freq))}","`ADS <{ads_link}>`__"\n')
+        #print(all_freq)