From 21768547dd7d8f24b2c17ecf22273204d64fb5bc Mon Sep 17 00:00:00 2001
From: Olivia Lynn <olynn@andrew.cmu.edu>
Date: Fri, 22 Dec 2023 16:53:47 -0500
Subject: [PATCH] Add short description of running pipelines w ceci shell cmd

---
 .../Build_Save_Load_Run_Pipeline.ipynb        | 44 +++++++++++--------
 1 file changed, 26 insertions(+), 18 deletions(-)

diff --git a/examples/core_examples/Build_Save_Load_Run_Pipeline.ipynb b/examples/core_examples/Build_Save_Load_Run_Pipeline.ipynb
index e174c16..460394a 100644
--- a/examples/core_examples/Build_Save_Load_Run_Pipeline.ipynb
+++ b/examples/core_examples/Build_Save_Load_Run_Pipeline.ipynb
@@ -8,7 +8,7 @@
     "\n",
     "**Author:** Eric Charles\n",
     "\n",
-    "**Last Run Successfully:** August 2, 2023"
+    "**Last Run Successfully:** December 22, 2023"
    ]
   },
   {
@@ -43,7 +43,7 @@
     "from rail.creation.engines.flowEngine import FlowCreator, FlowPosterior\n",
     "from rail.core.data import TableHandle\n",
     "from rail.core.stage import RailStage\n",
-    "from rail.core.util_stages import ColumnMapper, TableConverter\n"
+    "from rail.core.util_stages import ColumnMapper, TableConverter"
    ]
   },
   {
@@ -64,7 +64,7 @@
    "outputs": [],
    "source": [
     "DS = RailStage.data_store\n",
-    "DS.__class__.allow_overwrite = True\n"
+    "DS.__class__.allow_overwrite = True"
    ]
   },
   {
@@ -100,7 +100,7 @@
     "bands = [\"u\", \"g\", \"r\", \"i\", \"z\", \"y\"]\n",
     "band_dict = {band: f\"mag_{band}_lsst\" for band in bands}\n",
     "rename_dict = {f\"mag_{band}_lsst_err\": f\"mag_err_{band}_lsst\" for band in bands}\n",
-    "post_grid = [float(x) for x in np.linspace(0.0, 5, 21)]\n"
+    "post_grid = [float(x) for x in np.linspace(0.0, 5, 21)]"
    ]
   },
   {
@@ -147,7 +147,7 @@
     "\n",
     "table_conv_test = TableConverter.make_stage(\n",
     "    name=\"table_conv_test\", output_format=\"numpyDict\", seed=12345\n",
-    ")\n"
+    ")"
    ]
   },
   {
@@ -156,7 +156,7 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "flow_engine_test.sample(6, seed=0).data\n"
+    "flow_engine_test.sample(6, seed=0).data"
    ]
   },
   {
@@ -177,7 +177,7 @@
     "pipe = ceci.Pipeline.interactive()\n",
     "stages = [flow_engine_test, lsst_error_model_test, col_remapper_test, table_conv_test]\n",
     "for stage in stages:\n",
-    "    pipe.add_stage(stage)\n"
+    "    pipe.add_stage(stage)"
    ]
   },
   {
@@ -198,7 +198,7 @@
    "outputs": [],
    "source": [
     "# Get the names of the stages\n",
-    "pipe.stage_names\n"
+    "pipe.stage_names"
    ]
   },
   {
@@ -208,7 +208,7 @@
    "outputs": [],
    "source": [
     "# Get the configuration of a particular stage\n",
-    "pipe.flow_engine_test.config\n"
+    "pipe.flow_engine_test.config"
    ]
   },
   {
@@ -219,7 +219,7 @@
    "source": [
     "# Get the list of outputs 'tags'\n",
     "# These are how the stage thinks of the outputs, as a list names associated to DataHandle types.\n",
-    "pipe.flow_engine_test.outputs\n"
+    "pipe.flow_engine_test.outputs"
    ]
   },
   {
@@ -230,7 +230,7 @@
    "source": [
     "# Get the list of outputs 'aliased tags'\n",
     "# These are how the pipeline things of the outputs, as a unique key that points to a particular file\n",
-    "pipe.flow_engine_test._outputs\n"
+    "pipe.flow_engine_test._outputs"
    ]
   },
   {
@@ -252,7 +252,7 @@
     "lsst_error_model_test.connect_input(flow_engine_test)\n",
     "col_remapper_test.connect_input(lsst_error_model_test)\n",
     "# flow_post_test.connect_input(col_remapper_test, inputTag='input')\n",
-    "table_conv_test.connect_input(col_remapper_test)\n"
+    "table_conv_test.connect_input(col_remapper_test)"
    ]
   },
   {
@@ -278,7 +278,7 @@
    "source": [
     "pipe.initialize(\n",
     "    dict(model=flow_file), dict(output_dir=\".\", log_dir=\".\", resume=False), None\n",
-    ")\n"
+    ")"
    ]
   },
   {
@@ -300,7 +300,7 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "pipe.save(\"pipe_saved.yml\")\n"
+    "pipe.save(\"pipe_saved.yml\")"
    ]
   },
   {
@@ -316,7 +316,7 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "pr = ceci.Pipeline.read(\"pipe_saved.yml\")\n"
+    "pr = ceci.Pipeline.read(\"pipe_saved.yml\")"
    ]
   },
   {
@@ -334,7 +334,15 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "pr.run()\n"
+    "pr.run()"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "## Running saved pipelines from the command line\n",
+    "Once you've saved a pipeline and have the `pipeline_name.yml` and `pipeline_name_config.yml` file pair, you can go ahead and run the pipeline from the command line instead, if you prefer. With [ceci](https://github.com/LSSTDESC/ceci) installed in your environment, just run `ceci path/to/the/pipeline.yml`. Running the pipeline we've just made would look like:"
    ]
   },
   {
@@ -343,7 +351,7 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "pwd\n"
+    "! ceci pipe_saved.yml"
    ]
   }
  ],
@@ -363,7 +371,7 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.11.4"
+   "version": "3.11.6"
   },
   "vscode": {
    "interpreter": {