From c8ea3ac8d23a8fa36023e963e72aa442396d7ab1 Mon Sep 17 00:00:00 2001
From: Javier Cladellas <javiercladellas@gmail.com>
Date: Wed, 18 Dec 2024 14:32:11 +0100
Subject: [PATCH 01/11] factor and change default val

---
 src/feelpp/benchmarking/report/__main__.py | 26 +++++-----------------
 1 file changed, 6 insertions(+), 20 deletions(-)

diff --git a/src/feelpp/benchmarking/report/__main__.py b/src/feelpp/benchmarking/report/__main__.py
index 595b3ab9..00939355 100644
--- a/src/feelpp/benchmarking/report/__main__.py
+++ b/src/feelpp/benchmarking/report/__main__.py
@@ -12,7 +12,7 @@
 
 def main_cli():
     parser = argparse.ArgumentParser(description="Render all benchmarking reports")
-    parser.add_argument("--config_file", type=str, help="Path to the JSON config file", default="./src/feelpp/benchmarking/report/config/config.json")
+    parser.add_argument("--config_file", type=str, help="Path to the JSON config file", default="./reports/website_config.json")
     parser.add_argument("--json_output_path", type=str, help="Path to the output directory", default="reports")
     parser.add_argument("--modules_path", type=str, help="Path to the modules directory", default="./docs/modules/ROOT/pages")
     args = parser.parse_args()
@@ -39,26 +39,12 @@ def main_cli():
     with open("./src/feelpp/benchmarking/report/config/overviewConfig.json","r") as f:
         overview_config = json.load(f)
 
-    print("----- APPLICATIONS VIEW -------")
-    applications.printHierarchy()
-    applications.initModules(args.modules_path, index_renderer, parent_id="catalog-index")
-    applications.initOverviewModels(overview_config)
-    applications.createOverviews(args.modules_path,overview_renderer)
-    print("-------------------------------")
+    for repository in [applications,machines,use_cases]:
+        repository.printHierarchy()
+        repository.initModules(args.modules_path, index_renderer, parent_id="catalog-index")
+        repository.initOverviewModels(overview_config)
+        repository.createOverviews(args.modules_path,overview_renderer)
 
-    print("----- MACHINES VIEW -------")
-    machines.printHierarchy()
-    machines.initModules(args.modules_path, index_renderer, parent_id="catalog-index")
-    machines.initOverviewModels(overview_config)
-    machines.createOverviews(args.modules_path,overview_renderer)
-    print("-------------------------------")
-
-    print("----- USE CASES VIEW -------")
-    use_cases.printHierarchy()
-    use_cases.initModules(args.modules_path, index_renderer, parent_id="catalog-index")
-    use_cases.initOverviewModels(overview_config)
-    use_cases.createOverviews(args.modules_path,overview_renderer)
-    print("-------------------------------")
 
     report_renderer = RendererFactory.create("benchmark")
 

From 806880c6d662ffef5e0c2effa3044045b9063e07 Mon Sep 17 00:00:00 2001
From: Javier Cladellas <javiercladellas@gmail.com>
Date: Wed, 18 Dec 2024 15:00:44 +0100
Subject: [PATCH 02/11] split parser from main #160

---
 .../tutorial/pages/gettingstarted.adoc        |  6 +--
 src/feelpp/benchmarking/report/__main__.py    | 26 ++++-------
 src/feelpp/benchmarking/report/parser.py      | 46 +++++++++++++++++++
 3 files changed, 59 insertions(+), 19 deletions(-)
 create mode 100644 src/feelpp/benchmarking/report/parser.py

diff --git a/docs/modules/tutorial/pages/gettingstarted.adoc b/docs/modules/tutorial/pages/gettingstarted.adoc
index e5230d72..72d9311b 100644
--- a/docs/modules/tutorial/pages/gettingstarted.adoc
+++ b/docs/modules/tutorial/pages/gettingstarted.adoc
@@ -91,6 +91,6 @@ Once this file is located, users can run the `render-benchmarks` command to rend
 
 The script takes the following arguments:
 
-- `config_file` : The path of the website configuration file.
-- `json_output_path`: [Optional] Path of the directory to download the reports to. Only relevant if the configuration file contains remote locations (only Girder is supported at the moment).
-- `modules_path`: [Optional] Path to the Antora module to render the reports to. It defaults to _docs/modules/ROOT/pages_. Multiple directories will be recursively created under the provided path.
\ No newline at end of file
+- `config-file` : The path of the website configuration file.
+- `remote-download-dir`: [Optional] Path of the directory to download the reports to. Only relevant if the configuration file contains remote locations (only Girder is supported at the moment).
+- `modules-path`: [Optional] Path to the Antora module to render the reports to. It defaults to _docs/modules/ROOT/pages_. Multiple directories will be recursively created under the provided path.
\ No newline at end of file
diff --git a/src/feelpp/benchmarking/report/__main__.py b/src/feelpp/benchmarking/report/__main__.py
index 00939355..6182938c 100644
--- a/src/feelpp/benchmarking/report/__main__.py
+++ b/src/feelpp/benchmarking/report/__main__.py
@@ -7,21 +7,15 @@
 from feelpp.benchmarking.report.useCases.repository import UseCaseRepository
 
 from feelpp.benchmarking.report.renderer import RendererFactory
-
+from feelpp.benchmarking.report.parser import ReportArgParser
 
 
 def main_cli():
-    parser = argparse.ArgumentParser(description="Render all benchmarking reports")
-    parser.add_argument("--config_file", type=str, help="Path to the JSON config file", default="./reports/website_config.json")
-    parser.add_argument("--json_output_path", type=str, help="Path to the output directory", default="reports")
-    parser.add_argument("--modules_path", type=str, help="Path to the modules directory", default="./docs/modules/ROOT/pages")
-    args = parser.parse_args()
-
-    # Arguments treatment
-    json_output_path = args.json_output_path[:-1] if args.json_output_path[-1] == "/" else args.json_output_path
+    parser = ReportArgParser()
+    parser.printArgs()
 
-    config_handler = ConfigHandler(args.config_file)
-    girder_handler = GirderHandler(json_output_path)
+    config_handler = ConfigHandler(parser.args.config_file)
+    girder_handler = GirderHandler(parser.args.remote_download_dir)
 
     applications = ApplicationRepository(config_handler.applications)
     use_cases = UseCaseRepository(config_handler.use_cases)
@@ -36,17 +30,17 @@ def main_cli():
     index_renderer = RendererFactory.create("index")
     overview_renderer = RendererFactory.create("atomic_overview")
 
-    with open("./src/feelpp/benchmarking/report/config/overviewConfig.json","r") as f:
+    with open(parser.args.overview_config,"r") as f:
         overview_config = json.load(f)
 
     for repository in [applications,machines,use_cases]:
         repository.printHierarchy()
-        repository.initModules(args.modules_path, index_renderer, parent_id="catalog-index")
+        repository.initModules(parser.args.modules_path, index_renderer, parent_id="catalog-index")
         repository.initOverviewModels(overview_config)
-        repository.createOverviews(args.modules_path,overview_renderer)
+        repository.createOverviews(parser.args.modules_path,overview_renderer)
 
 
     report_renderer = RendererFactory.create("benchmark")
 
-    atomic_reports.movePartials(os.path.join(args.modules_path,"descriptions"))
-    atomic_reports.createReports(os.path.join(args.modules_path,"reports"),report_renderer)
\ No newline at end of file
+    atomic_reports.movePartials(os.path.join(parser.args.modules_path,"descriptions"))
+    atomic_reports.createReports(os.path.join(parser.args.modules_path,"reports"),report_renderer)
\ No newline at end of file
diff --git a/src/feelpp/benchmarking/report/parser.py b/src/feelpp/benchmarking/report/parser.py
new file mode 100644
index 00000000..11a2d85d
--- /dev/null
+++ b/src/feelpp/benchmarking/report/parser.py
@@ -0,0 +1,46 @@
+from argparse import ArgumentParser, RawTextHelpFormatter
+from feelpp.benchmarking.reframe.parser import CustomHelpFormatter
+import os, shutil
+
+
+#TODO: Factorize with feelpp.reframe parser
+class ReportArgParser():
+    """ Class for parsing and validating command-line arguments for the report module"""
+    def __init__(self):
+        self.parser = ArgumentParser(formatter_class=CustomHelpFormatter, add_help=False,description="Render benchmarking reports")
+        self.addArgs()
+        self.args = self.parser.parse_args()
+
+    def addArgs(self):
+        """ Add arguments to the parser """
+        self.parser.add_argument("--config-file", "-c", type=str, help="Path to the JSON config file", default="./reports/website_config.json")
+        self.parser.add_argument("--remote-download-dir", "-do", type=str, help="Path to the output directory where remote reports will be downloaded", default="reports")
+        self.parser.add_argument("--modules-path", "-m", type=str, help="Path to the modules directory where reports will be rendered", default="./docs/modules/ROOT/pages")
+        self.parser.add_argument("--plot-configs", "-pc", type=str, nargs='+', action='extend', help="Path the a plot configuration to use for a given benchmark. To be used along with --patch-reports")
+        self.parser.add_argument("--overview-config", "-oc", type=str, help="Path to the overview configuration file", default="./src/feelpp/benchmarking/report/config/overviewConfig.json")
+
+    def checkDirectoriesExist(self):
+        """ Check that directories passed as arguments exist in the filesystem"""
+        for filepath in [self.args.config_file, self.args.overview_config,self.args.modules_path]:
+            if not os.path.exists(filepath):
+                raise FileNotFoundError(f"File not found ({filepath})")
+
+        for plot_config in self.args.plot_configs:
+            if not os.path.exists(plot_config):
+                raise FileNotFoundError(f"Modules path not found ({plot_config})")
+
+    def normalizePaths(self):
+        """Normalize paths passed as arguments"""
+        self.args.config_file = os.path.normpath(self.args.remote_download_dir)
+        self.args.remote_download_dir = os.path.normpath(self.args.remote_download_dir)
+        self.args.modules_path = os.path.normpath(self.args.modules_path)
+        self.args.overview_config = os.path.normpath(self.args.overview_config)
+        self.args.plot_configs = [os.path.normpath(plot_config) for plot_config in self.args.plot_configs]
+
+
+    def printArgs(self):
+        """ Prints arguments on the standard output"""
+        print("\n[Loaded command-line options]")
+        for arg in vars(self.args):
+            print(f"\t > {arg + ':' :<{20}} {getattr(self.args, arg)}")
+        print("\n" + '=' * shutil.get_terminal_size().columns)
\ No newline at end of file

From 80542b0eb5644cd2fd8b73088b4035fe19562c0f Mon Sep 17 00:00:00 2001
From: Javier Cladellas <javiercladellas@gmail.com>
Date: Wed, 18 Dec 2024 17:18:44 +0100
Subject: [PATCH 03/11] add replacePlotConfig method #160

---
 .../benchmarking/report/atomicReports/atomicReport.py      | 7 +++++++
 1 file changed, 7 insertions(+)

diff --git a/src/feelpp/benchmarking/report/atomicReports/atomicReport.py b/src/feelpp/benchmarking/report/atomicReports/atomicReport.py
index b437d817..f2db1b16 100644
--- a/src/feelpp/benchmarking/report/atomicReports/atomicReport.py
+++ b/src/feelpp/benchmarking/report/atomicReports/atomicReport.py
@@ -18,6 +18,7 @@ def __init__(self, application_id, machine_id, use_case_id, reframe_report_json,
             partials_dir (str): The directory path where parametric descriptions of the use case can be found (usually comes with the reframe report). Pass None if non-existent
         """
         data = self.parseJson(reframe_report_json)
+        self.plots_config_path = plot_config_json
         self.plots_config = self.parseJson(plot_config_json)
         self.partials_dir = partials_dir
 
@@ -41,6 +42,12 @@ def __init__(self, application_id, machine_id, use_case_id, reframe_report_json,
 
         self.model = AtomicReportModel(self.runs)
 
+    def replacePlotsConfig(self,plot_config_json,save=False):
+        self.plots_config = self.parseJson(plot_config_json)
+        if save:
+            with open(self.plots_config_path, "w") as old_f, open(plot_config_json,"r") as new_f:
+                old_f.write(new_f.read())
+
     def setIndexes(self, application, machine, use_case):
         """ Set the indexes for the atomic report.
         Along with the date, they should form a unique identifier for the report.

From 0c7f3550e3381522551316a6e750a6674252c37f Mon Sep 17 00:00:00 2001
From: Javier Cladellas <javiercladellas@gmail.com>
Date: Wed, 18 Dec 2024 17:19:09 +0100
Subject: [PATCH 04/11] add validation and save patches option #160

---
 src/feelpp/benchmarking/report/parser.py | 33 +++++++++++++++++++-----
 1 file changed, 27 insertions(+), 6 deletions(-)

diff --git a/src/feelpp/benchmarking/report/parser.py b/src/feelpp/benchmarking/report/parser.py
index 11a2d85d..96a78d65 100644
--- a/src/feelpp/benchmarking/report/parser.py
+++ b/src/feelpp/benchmarking/report/parser.py
@@ -10,14 +10,35 @@ def __init__(self):
         self.parser = ArgumentParser(formatter_class=CustomHelpFormatter, add_help=False,description="Render benchmarking reports")
         self.addArgs()
         self.args = self.parser.parse_args()
+        self.validate()
+        self.normalizePaths()
 
     def addArgs(self):
         """ Add arguments to the parser """
         self.parser.add_argument("--config-file", "-c", type=str, help="Path to the JSON config file", default="./reports/website_config.json")
         self.parser.add_argument("--remote-download-dir", "-do", type=str, help="Path to the output directory where remote reports will be downloaded", default="reports")
         self.parser.add_argument("--modules-path", "-m", type=str, help="Path to the modules directory where reports will be rendered", default="./docs/modules/ROOT/pages")
-        self.parser.add_argument("--plot-configs", "-pc", type=str, nargs='+', action='extend', help="Path the a plot configuration to use for a given benchmark. To be used along with --patch-reports")
-        self.parser.add_argument("--overview-config", "-oc", type=str, help="Path to the overview configuration file", default="./src/feelpp/benchmarking/report/config/overviewConfig.json")
+        self.parser.add_argument("--overview-config", "-oc", type=str, help="Path to the overview configuration file", default="./src/feelpp/benchmarking/report/config/overviewConfig.json"),
+        self.parser.add_argument("--plot-configs", "-pc", type=str, nargs='+',default=[], action='extend', help="Path the a plot configuration to use for a given benchmark. To be used along with --patch-reports")
+        self.parser.add_argument("--patch-reports","-pr", type=str, nargs='+',default=[], action='extend', help="Id of the reports to path, the syntax of the id is machine-application-usecase-date e.g. gaya-feelpp_app-my_use_case-2024_11_05T01_05_32. It is possible to affect all reports in a component by replacing the machine, application, use_case or date by 'all'. Also, one can indicate to patch the latest report by replacing the date by 'latest'. If this option is not provided but plot-configs is, then the latest report will be patched (most recent report date)")
+        self.parser.add_argument("--save-patches","-sp", action='store_true', help="If this flag is active, existing plot configurations will be replaced with the ones provided in patch-reports.")
+
+    def validate(self):
+        """ Validate specific options """
+        self.checkDirectoriesExist()
+
+        if self.args.patch_reports:
+            for patch_report in self.args.patch_reports:
+                splitted_patch = patch_report.split("-")
+                if len(splitted_patch) != 4:
+                    raise ValueError(f"The ID syntaxt is incorrect ({patch_report})")
+                machine, app, use_case, date = splitted_patch
+                if "latest" in [machine,app,use_case]:
+                    raise ValueError("Latest not accepted for that component")
+                if machine == "all":
+                    raise ValueError("The machine component patch does not support the 'all' keyworkd")
+
+            self.args.patch_reports = [patch_report.split("-") for patch_report in self.args.patch_reports]
 
     def checkDirectoriesExist(self):
         """ Check that directories passed as arguments exist in the filesystem"""
@@ -25,13 +46,13 @@ def checkDirectoriesExist(self):
             if not os.path.exists(filepath):
                 raise FileNotFoundError(f"File not found ({filepath})")
 
-        for plot_config in self.args.plot_configs:
-            if not os.path.exists(plot_config):
-                raise FileNotFoundError(f"Modules path not found ({plot_config})")
+        for file in self.args.plot_configs:
+            if not os.path.exists(file):
+                raise FileNotFoundError(f"File not found ({file})")
 
     def normalizePaths(self):
         """Normalize paths passed as arguments"""
-        self.args.config_file = os.path.normpath(self.args.remote_download_dir)
+        self.args.config_file = os.path.normpath(self.args.config_file)
         self.args.remote_download_dir = os.path.normpath(self.args.remote_download_dir)
         self.args.modules_path = os.path.normpath(self.args.modules_path)
         self.args.overview_config = os.path.normpath(self.args.overview_config)

From 735c6d5cd51aa8bb653b3164e0e55ca36d0f66ea Mon Sep 17 00:00:00 2001
From: Javier Cladellas <javiercladellas@gmail.com>
Date: Wed, 18 Dec 2024 17:19:25 +0100
Subject: [PATCH 05/11] add repository method to patch plots config #160

---
 src/feelpp/benchmarking/report/__main__.py    |  5 +-
 .../report/atomicReports/repository.py        | 47 ++++++++++++++++++-
 2 files changed, 50 insertions(+), 2 deletions(-)

diff --git a/src/feelpp/benchmarking/report/__main__.py b/src/feelpp/benchmarking/report/__main__.py
index 6182938c..d49531b9 100644
--- a/src/feelpp/benchmarking/report/__main__.py
+++ b/src/feelpp/benchmarking/report/__main__.py
@@ -1,4 +1,4 @@
-import argparse, os, json
+import os, json
 
 from feelpp.benchmarking.report.config.handlers import ConfigHandler, GirderHandler
 from feelpp.benchmarking.report.atomicReports.repository import AtomicReportRepository
@@ -33,6 +33,9 @@ def main_cli():
     with open(parser.args.overview_config,"r") as f:
         overview_config = json.load(f)
 
+    if parser.args.plot_configs:
+        atomic_reports.patchPlotConfigs(parser.args.plot_configs, parser.args.patch_report_ids, parser.args.save_patches)
+
     for repository in [applications,machines,use_cases]:
         repository.printHierarchy()
         repository.initModules(parser.args.modules_path, index_renderer, parent_id="catalog-index")
diff --git a/src/feelpp/benchmarking/report/atomicReports/repository.py b/src/feelpp/benchmarking/report/atomicReports/repository.py
index 463efc4c..5d3294cc 100644
--- a/src/feelpp/benchmarking/report/atomicReports/repository.py
+++ b/src/feelpp/benchmarking/report/atomicReports/repository.py
@@ -1,6 +1,7 @@
 from feelpp.benchmarking.report.atomicReports.atomicReport import AtomicReport
 from feelpp.benchmarking.report.base.repository import Repository
 import os
+from datetime import datetime
 
 class AtomicReportRepository(Repository):
     """ Repository for atomic reports """
@@ -144,4 +145,48 @@ def movePartials(self,base_dir):
             os.mkdir(base_dir)
 
         for atomic_report in self.data:
-            atomic_report.movePartials(base_dir)
\ No newline at end of file
+            atomic_report.movePartials(base_dir)
+
+
+    def patchPlotConfigs(self,plot_configs, patch_reports_ids, save = False):
+        """ Replaces the plot configuration with a new one.
+        TODO: explain Cases (1 plot_config; many patches, ...)
+        Args:
+            plot_configs (list[str]): list of filepaths containing the new plot configuration.
+            patch_reports_ids (list[str] ): list of report ids to filter patching, following the syntax machine-application-usecase-date. The date componenent accept the 'latest' keyword, and the application, use case and date component accept the 'all' keyword. If the list is empty, the latest report will be patched.
+            save (bool): If true, it will replace the file contents of the old plots configuration
+        """
+        if plot_configs:
+            if not patch_reports_ids: # 1 plot config, No reports to patch (select latest)
+                latest_report = max(self.data, key=lambda report: datetime.strptime(report.date, "%Y-%m-%dT%H:%M:%S%z"))
+                latest_report.replacePlotsConfig(plot_configs[0], save)
+            else:
+                for i,patch_report in patch_reports_ids:
+                    #Filter reports based on ids
+                    patch_machine, patch_application, patch_usecase, patch_date = patch_report
+                    patch_machine_reports = list(filter(lambda x: x.machine_id == patch_machine, self.data.data))
+
+                    if patch_application == "all":
+                        patch_application_reports = patch_machine_reports
+                    else:
+                        patch_application_reports = list(filter(lambda x: x.application_id == patch_application, patch_machine_reports))
+
+                    if patch_usecase == "all":
+                        patch_usecase_reports = patch_application_reports
+                    else:
+                        patch_usecase_reports = list(filter(lambda x: x.use_case_id == patch_usecase, patch_application_reports))
+
+                    if patch_date == "all":
+                        reports_to_patch = patch_usecase_reports
+                    elif patch_date == "latest":
+                        reports_to_patch = [max(patch_usecase_reports, key=lambda report: datetime.strptime(report.date, "%Y-%m-%dT%H:%M:%S%z"))]
+                    else:
+                        reports_to_patch = list(filter(lambda x: datetime.strptime(x.date,"%Y-%m-%dT%H:%M:%S%z").strftime("%Y_%m_%dT%H_%M_%S") == patch_date ))
+
+                    for report_to_patch in reports_to_patch:
+                        #1 plot config, many reports to patch
+                        #Same number of plot config as reports to patch
+                        plot_config = plot_configs[i] if len(patch_reports_ids) == len(plot_configs) else plot_configs[0] if len(plot_configs) == 1 else False
+                        if not plot_config:
+                            raise ValueError("Plots configuration must be either of length 1 or exactly the same lenght as patches")
+                        report_to_patch.replacePlotsConfig(plot_config,save)

From 49af1582e0f24a4af5d1ee9a33b8de3e136472ed Mon Sep 17 00:00:00 2001
From: Javier Cladellas <javiercladellas@gmail.com>
Date: Wed, 18 Dec 2024 17:23:31 +0100
Subject: [PATCH 06/11] config_file -> config-file #160

---
 .github/workflows/ci.yml                    | 4 ++--
 netlify-build.sh                            | 2 +-
 src/feelpp/benchmarking/reframe/__main__.py | 2 +-
 3 files changed, 4 insertions(+), 4 deletions(-)

diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml
index 139de6fa..5a5410f4 100644
--- a/.github/workflows/ci.yml
+++ b/.github/workflows/ci.yml
@@ -64,7 +64,7 @@ jobs:
     - name: Dry-run reports
       run: |
         source .venv/bin/activate
-        render-benchmarks --config_file reports/website_config.json
+        render-benchmarks --config-file reports/website_config.json
     - name: Check files
       run: | #TODO: check if not empty (maybe)
         nb_rfm_report_files=$(ls -1q reports/parallelSum/parallel_sum/gaya|wc -l)
@@ -109,7 +109,7 @@ jobs:
     - name: Render reports
       run: |
         source .venv/bin/activate
-        render-benchmarks --config_file=./tmp/website_config.json
+        render-benchmarks --config-file=./tmp/website_config.json
       env:
         GIRDER_API_KEY: ${{ secrets.GIRDER }}
     - name: Build Antora Site
diff --git a/netlify-build.sh b/netlify-build.sh
index 245f45fa..7c866b10 100755
--- a/netlify-build.sh
+++ b/netlify-build.sh
@@ -17,5 +17,5 @@ else
     echo "Downloading Production benchmarks"
     girder-download -gid $production_website_config_id -o ./tmp/ -fn website_config.json
 fi
-render-benchmarks --config_file=./tmp/website_config.json
+render-benchmarks --config-file=./tmp/website_config.json
 npx antora --stacktrace generate --cache-dir cache --clean --html-url-extension-style=indexify site.yml
diff --git a/src/feelpp/benchmarking/reframe/__main__.py b/src/feelpp/benchmarking/reframe/__main__.py
index fb691959..db26f768 100644
--- a/src/feelpp/benchmarking/reframe/__main__.py
+++ b/src/feelpp/benchmarking/reframe/__main__.py
@@ -130,7 +130,7 @@ def main_cli():
         #======================================================#
 
     if parser.args.website:
-        subprocess.run(["render-benchmarks","--config_file", website_config.config_filepath])
+        subprocess.run(["render-benchmarks","--config-file", website_config.config_filepath])
         subprocess.run(["npm","run","antora"])
         subprocess.run(["npm","run","start"])
 

From aacea53df941f0cc4885b676bc9600329e5cea96 Mon Sep 17 00:00:00 2001
From: Javier Cladellas <javiercladellas@gmail.com>
Date: Thu, 19 Dec 2024 09:31:07 +0100
Subject: [PATCH 07/11] use time start instead of time end #160

---
 src/feelpp/benchmarking/report/templates/benchmark.adoc.j2 | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/src/feelpp/benchmarking/report/templates/benchmark.adoc.j2 b/src/feelpp/benchmarking/report/templates/benchmark.adoc.j2
index ad11d3c5..5d338a94 100644
--- a/src/feelpp/benchmarking/report/templates/benchmark.adoc.j2
+++ b/src/feelpp/benchmarking/report/templates/benchmark.adoc.j2
@@ -3,7 +3,7 @@
 :page-jupyter: true
 :page-tags: toolbox, catalog
 :parent-catalogs: {{parent_catalogs}}
-:description: Performance report for {{ machine_display_name }} on {{ session_info.time_end }}
+:description: Performance report for {{ machine_display_name }} on {{ session_info.time_start }}
 :page-illustration: {{ machine_id }}.jpg
 :author: Your Name
 :revdate: {{ session_info.time_end }}

From be30cf5b1a21fbd43313d1c56bfcca01f4ecd9fd Mon Sep 17 00:00:00 2001
From: Javier Cladellas <javiercladellas@gmail.com>
Date: Thu, 19 Dec 2024 09:34:19 +0100
Subject: [PATCH 08/11] bug fixes #160

---
 src/feelpp/benchmarking/report/__main__.py                 | 2 +-
 .../benchmarking/report/atomicReports/atomicReport.py      | 7 ++++---
 src/feelpp/benchmarking/report/atomicReports/repository.py | 6 +++---
 3 files changed, 8 insertions(+), 7 deletions(-)

diff --git a/src/feelpp/benchmarking/report/__main__.py b/src/feelpp/benchmarking/report/__main__.py
index d49531b9..4a086c1e 100644
--- a/src/feelpp/benchmarking/report/__main__.py
+++ b/src/feelpp/benchmarking/report/__main__.py
@@ -34,7 +34,7 @@ def main_cli():
         overview_config = json.load(f)
 
     if parser.args.plot_configs:
-        atomic_reports.patchPlotConfigs(parser.args.plot_configs, parser.args.patch_report_ids, parser.args.save_patches)
+        atomic_reports.patchPlotConfigs(parser.args.plot_configs, parser.args.patch_reports, parser.args.save_patches)
 
     for repository in [applications,machines,use_cases]:
         repository.printHierarchy()
diff --git a/src/feelpp/benchmarking/report/atomicReports/atomicReport.py b/src/feelpp/benchmarking/report/atomicReports/atomicReport.py
index f2db1b16..dc143a3b 100644
--- a/src/feelpp/benchmarking/report/atomicReports/atomicReport.py
+++ b/src/feelpp/benchmarking/report/atomicReports/atomicReport.py
@@ -43,10 +43,11 @@ def __init__(self, application_id, machine_id, use_case_id, reframe_report_json,
         self.model = AtomicReportModel(self.runs)
 
     def replacePlotsConfig(self,plot_config_json,save=False):
-        self.plots_config = self.parseJson(plot_config_json)
+        print(f"Patching plots for {self.machine_id}-{self.application_id}-{self.use_case_id}-{self.date} with {plot_config_json}")
+        self.plots_config = self.parseJson(plot_config_json)["plots"]
         if save:
-            with open(self.plots_config_path, "w") as old_f, open(plot_config_json,"r") as new_f:
-                old_f.write(new_f.read())
+            with open(self.plots_config_path, "w") as old_f:
+                json.dump(self.plots_config,old_f)
 
     def setIndexes(self, application, machine, use_case):
         """ Set the indexes for the atomic report.
diff --git a/src/feelpp/benchmarking/report/atomicReports/repository.py b/src/feelpp/benchmarking/report/atomicReports/repository.py
index 5d3294cc..bfff1f85 100644
--- a/src/feelpp/benchmarking/report/atomicReports/repository.py
+++ b/src/feelpp/benchmarking/report/atomicReports/repository.py
@@ -161,10 +161,10 @@ def patchPlotConfigs(self,plot_configs, patch_reports_ids, save = False):
                 latest_report = max(self.data, key=lambda report: datetime.strptime(report.date, "%Y-%m-%dT%H:%M:%S%z"))
                 latest_report.replacePlotsConfig(plot_configs[0], save)
             else:
-                for i,patch_report in patch_reports_ids:
+                for i,patch_report in enumerate(patch_reports_ids):
                     #Filter reports based on ids
                     patch_machine, patch_application, patch_usecase, patch_date = patch_report
-                    patch_machine_reports = list(filter(lambda x: x.machine_id == patch_machine, self.data.data))
+                    patch_machine_reports = list(filter(lambda x: x.machine_id == patch_machine, self.data))
 
                     if patch_application == "all":
                         patch_application_reports = patch_machine_reports
@@ -181,7 +181,7 @@ def patchPlotConfigs(self,plot_configs, patch_reports_ids, save = False):
                     elif patch_date == "latest":
                         reports_to_patch = [max(patch_usecase_reports, key=lambda report: datetime.strptime(report.date, "%Y-%m-%dT%H:%M:%S%z"))]
                     else:
-                        reports_to_patch = list(filter(lambda x: datetime.strptime(x.date,"%Y-%m-%dT%H:%M:%S%z").strftime("%Y_%m_%dT%H_%M_%S") == patch_date ))
+                        reports_to_patch = list(filter(lambda x: datetime.strptime(x.date,"%Y-%m-%dT%H:%M:%S%z").strftime("%Y_%m_%dT%H_%M_%S") == patch_date, patch_usecase_reports))
 
                     for report_to_patch in reports_to_patch:
                         #1 plot config, many reports to patch

From 93cb727fa9364f61a45b2dfcb43c9276645259a3 Mon Sep 17 00:00:00 2001
From: Javier Cladellas <javiercladellas@gmail.com>
Date: Thu, 19 Dec 2024 09:37:10 +0100
Subject: [PATCH 09/11] add --website flag to automatically compile antora docs
 and start http server #160

---
 src/feelpp/benchmarking/report/__main__.py | 8 ++++++--
 src/feelpp/benchmarking/report/parser.py   | 1 +
 2 files changed, 7 insertions(+), 2 deletions(-)

diff --git a/src/feelpp/benchmarking/report/__main__.py b/src/feelpp/benchmarking/report/__main__.py
index 4a086c1e..987ddaf0 100644
--- a/src/feelpp/benchmarking/report/__main__.py
+++ b/src/feelpp/benchmarking/report/__main__.py
@@ -1,4 +1,4 @@
-import os, json
+import os, json, subprocess
 
 from feelpp.benchmarking.report.config.handlers import ConfigHandler, GirderHandler
 from feelpp.benchmarking.report.atomicReports.repository import AtomicReportRepository
@@ -46,4 +46,8 @@ def main_cli():
     report_renderer = RendererFactory.create("benchmark")
 
     atomic_reports.movePartials(os.path.join(parser.args.modules_path,"descriptions"))
-    atomic_reports.createReports(os.path.join(parser.args.modules_path,"reports"),report_renderer)
\ No newline at end of file
+    atomic_reports.createReports(os.path.join(parser.args.modules_path,"reports"),report_renderer)
+
+    if parser.args.website:
+        subprocess.run(["npm","run","antora"])
+        subprocess.run(["npm","run","start"])
diff --git a/src/feelpp/benchmarking/report/parser.py b/src/feelpp/benchmarking/report/parser.py
index 96a78d65..011db185 100644
--- a/src/feelpp/benchmarking/report/parser.py
+++ b/src/feelpp/benchmarking/report/parser.py
@@ -22,6 +22,7 @@ def addArgs(self):
         self.parser.add_argument("--plot-configs", "-pc", type=str, nargs='+',default=[], action='extend', help="Path the a plot configuration to use for a given benchmark. To be used along with --patch-reports")
         self.parser.add_argument("--patch-reports","-pr", type=str, nargs='+',default=[], action='extend', help="Id of the reports to path, the syntax of the id is machine-application-usecase-date e.g. gaya-feelpp_app-my_use_case-2024_11_05T01_05_32. It is possible to affect all reports in a component by replacing the machine, application, use_case or date by 'all'. Also, one can indicate to patch the latest report by replacing the date by 'latest'. If this option is not provided but plot-configs is, then the latest report will be patched (most recent report date)")
         self.parser.add_argument("--save-patches","-sp", action='store_true', help="If this flag is active, existing plot configurations will be replaced with the ones provided in patch-reports.")
+        self.parser.add_argument("--website","-w", action='store_true', help="Compile documentation and start HTTP server with benchmark reports")
 
     def validate(self):
         """ Validate specific options """

From 36d319c2733ec5ae1123e58dc1ebc91de19479f4 Mon Sep 17 00:00:00 2001
From: Javier Cladellas <javiercladellas@gmail.com>
Date: Thu, 19 Dec 2024 09:39:02 +0100
Subject: [PATCH 10/11] change patches ids separator ("-" to ":")

---
 src/feelpp/benchmarking/report/parser.py | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/src/feelpp/benchmarking/report/parser.py b/src/feelpp/benchmarking/report/parser.py
index 011db185..9c48484e 100644
--- a/src/feelpp/benchmarking/report/parser.py
+++ b/src/feelpp/benchmarking/report/parser.py
@@ -20,7 +20,7 @@ def addArgs(self):
         self.parser.add_argument("--modules-path", "-m", type=str, help="Path to the modules directory where reports will be rendered", default="./docs/modules/ROOT/pages")
         self.parser.add_argument("--overview-config", "-oc", type=str, help="Path to the overview configuration file", default="./src/feelpp/benchmarking/report/config/overviewConfig.json"),
         self.parser.add_argument("--plot-configs", "-pc", type=str, nargs='+',default=[], action='extend', help="Path the a plot configuration to use for a given benchmark. To be used along with --patch-reports")
-        self.parser.add_argument("--patch-reports","-pr", type=str, nargs='+',default=[], action='extend', help="Id of the reports to path, the syntax of the id is machine-application-usecase-date e.g. gaya-feelpp_app-my_use_case-2024_11_05T01_05_32. It is possible to affect all reports in a component by replacing the machine, application, use_case or date by 'all'. Also, one can indicate to patch the latest report by replacing the date by 'latest'. If this option is not provided but plot-configs is, then the latest report will be patched (most recent report date)")
+        self.parser.add_argument("--patch-reports","-pr", type=str, nargs='+',default=[], action='extend', help="Id of the reports to path, the syntax of the id is machine:application:usecase:date e.g. gaya:feelpp_app:my_use_case:2024_11_05T01_05_32. It is possible to affect all reports in a component by replacing the machine, application, use_case or date by 'all'. Also, one can indicate to patch the latest report by replacing the date by 'latest'. If this option is not provided but plot-configs is, then the latest report will be patched (most recent report date)")
         self.parser.add_argument("--save-patches","-sp", action='store_true', help="If this flag is active, existing plot configurations will be replaced with the ones provided in patch-reports.")
         self.parser.add_argument("--website","-w", action='store_true', help="Compile documentation and start HTTP server with benchmark reports")
 
@@ -30,7 +30,7 @@ def validate(self):
 
         if self.args.patch_reports:
             for patch_report in self.args.patch_reports:
-                splitted_patch = patch_report.split("-")
+                splitted_patch = patch_report.split(":")
                 if len(splitted_patch) != 4:
                     raise ValueError(f"The ID syntaxt is incorrect ({patch_report})")
                 machine, app, use_case, date = splitted_patch
@@ -39,7 +39,7 @@ def validate(self):
                 if machine == "all":
                     raise ValueError("The machine component patch does not support the 'all' keyworkd")
 
-            self.args.patch_reports = [patch_report.split("-") for patch_report in self.args.patch_reports]
+            self.args.patch_reports = [patch_report.split(":") for patch_report in self.args.patch_reports]
 
     def checkDirectoriesExist(self):
         """ Check that directories passed as arguments exist in the filesystem"""

From fc7c65e50923249eeafc6ca7277a007430bf8ac5 Mon Sep 17 00:00:00 2001
From: Javier Cladellas <javiercladellas@gmail.com>
Date: Thu, 19 Dec 2024 09:42:42 +0100
Subject: [PATCH 11/11] exception #160

---
 src/feelpp/benchmarking/report/atomicReports/repository.py | 2 ++
 1 file changed, 2 insertions(+)

diff --git a/src/feelpp/benchmarking/report/atomicReports/repository.py b/src/feelpp/benchmarking/report/atomicReports/repository.py
index bfff1f85..ae101d05 100644
--- a/src/feelpp/benchmarking/report/atomicReports/repository.py
+++ b/src/feelpp/benchmarking/report/atomicReports/repository.py
@@ -158,6 +158,8 @@ def patchPlotConfigs(self,plot_configs, patch_reports_ids, save = False):
         """
         if plot_configs:
             if not patch_reports_ids: # 1 plot config, No reports to patch (select latest)
+                if len(plot_configs)>1:
+                    raise ValueError("When no patch reports are provided, plot configuration should be of length one")
                 latest_report = max(self.data, key=lambda report: datetime.strptime(report.date, "%Y-%m-%dT%H:%M:%S%z"))
                 latest_report.replacePlotsConfig(plot_configs[0], save)
             else: